OBO-Edit 2.3.1
15:04:2021 22:57
PSI-MI
1.2
pporras
CVversion: 2.5.5
Each of the top level terms in this file is the root term of an independent controlled vocabulary
Notes:
The PSI MI schema defines short labels for controlled vocabulary terms
The correct use of these vocabularies in the PSI Molecular Interaction XML schema is
The last accession number used in this file is stored in a separate file,
The maintenance of this file is ensured by Luana Licata luana.licata@uniroma2.it and Sandra Orchard orchard@ebi.ac.uk
coverage: This file collect controlled vocabularies describing different aspects of molecular interactions.
formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml.
mapping an element of the PSI Molecular Interaction XML schema.
psi-mi.lastac. It MUST be updated when this file is updated.
publisher: This file is published by the PSI MI working group see http://psidev.info/MI
short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.
definition
Label from MS DeltaMass
Drugable Genome Project
Alternate label curated by PSI-MI
Unique short label curated by PSI-MI
Subset of PSI-MI
Alternate label curated by PSI-MOD
Unique short label curated by PSI-MOD
subset of protein modifications
Agreed label from MS community
Alternate name from RESID
Misnomer label from RESID
Name from RESID
Systematic name from RESID
Alternate name from UniMod
Description (full_name) from UniMod
Interim label from UniMod
Label (title) from UniMod
Protein feature description from UniProtKB
subset_property
synonym_type_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
mi
PSI-MI
MI:0000
molecular interaction
Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
PMID:14755292
mi
Method to determine the interaction.
interaction detect
PSI-MI
MI:0001
interaction detection method
Method to determine the interaction.
PMID:14755292
interaction detect
Method to determine the molecules involved in the interaction.
participant detection
participant ident
PSI-MI
MI:0002
participant identification method
Method to determine the molecules involved in the interaction.
PMID:14755292
participant detection
participant ident
Method to determine the features of the proteins involved in the interaction.
feature detection
PSI-MI
MI:0003
feature detection method
Method to determine the features of the proteins involved in the interaction.
PMID:14755292
feature detection
This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
Affinity purification
affinity chrom
PSI-MI
MI:0004
affinity chromatography technology
This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
PMID:7708014
Affinity purification
affinity chrom
This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
PSI-MI
MI:0005
alanine scanning
This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
PMID:14755292
A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
anti bait coip
PSI-MI
MI:0006
anti bait coimmunoprecipitation
A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
PMID:7708014
anti bait coip
A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
anti tag coip
PSI-MI
MI:0007
anti tag coimmunoprecipitation
A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
PMID:7708014
anti tag coip
In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
PSI-MI
MI:0008
array technology
In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
PMID:14755292
The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
PSI-MI
MI:0009
bacterial display
The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
PMID:10436088
PMID:8248129
Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
beta galactosidase
PSI-MI
MI:0010
beta galactosidase complementation
Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
PMID:12042868
PMID:9237989
beta galactosidase
This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
beta lactamase
PSI-MI
MI:0011
beta lactamase complementation
This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
PMID:12042868
beta lactamase
In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
BRET
LRET
bret
PSI-MI
MI:0012
bioluminescence resonance energy transfer
In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
PMID:10725388
PMID:9874787
BRET
LRET
bret
The application of physical principles and methods to biological experiments.
PSI-MI
MI:0013
biophysical
The application of physical principles and methods to biological experiments.
PMID:14755292
Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
adenylate cyclase
bacterial two-hybrid
PSI-MI
MI:0014
adenylate cyclase complementation
Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
PMID:9576956
adenylate cyclase
bacterial two-hybrid
Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
CD
cd
PSI-MI
MI:0016
circular dichroism
Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
PMID:11578931
CD
cd
Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
fluorescence spectr
PSI-MI
MI:0017
classical fluorescence spectroscopy
Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
PMID:7708014
fluorescence spectr
The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
2 hybrid
2-hybrid
2H
2h
Gal4 transcription regeneration
Y2H
classical two hybrid
two-hybrid
yeast two hybrid
PSI-MI
Y-2H
MI:0018
two hybrid
The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
PMID:10967325
PMID:12634794
PMID:1946372
2 hybrid
2-hybrid
2H
2h
Gal4 transcription regeneration
classical two hybrid
two-hybrid
yeast two hybrid
In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
Co-IP
CoIp
co-immunoprecipitation
coip
immunoprecipitation
PSI-MI
MI:0019
coimmunoprecipitation
In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
PMID:7708014
Co-IP
CoIp
co-immunoprecipitation
coip
immunoprecipitation
Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
tem
PSI-MI
MI:0020
transmission electron microscopy
Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
PMID:14755292
tem
Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.
OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
coloc fluoresc probe
PSI-MI
MI:0021
colocalization by fluorescent probes cloning
true
Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.
OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
PMID:14755292
coloc fluoresc probe
The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.
OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
Immunofluorescence Staining
Immunostaining
coloc immunostaining
PSI-MI
MI:0022
colocalization by immunostaining
true
The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.
OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
PMID:14755292
Immunofluorescence Staining
Immunostaining
coloc immunostaining
Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.
OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
coloc visual technol
PSI-MI
MI:0023
colocalization/visualisation technologies
true
Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.
OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
PMID:14755292
coloc visual technol
Text mining is used to support interactions which have been determined by other methods.
conformational tm
PSI-MI
MI:0024
confirmational text mining
Text mining is used to support interactions which have been determined by other methods.
PMID:14755292
conformational tm
Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.
OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
PSI-MI
MI:0025
copurification
true
Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.
OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
PMID:14755292
Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
PSI-MI
MI:0026
correlated mutations
Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
PMID:11933068
Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
PSI-MI
MI:0027
cosedimentation
Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
PMID:14755292
The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
solution sedimentati
PSI-MI
MI:0028
cosedimentation in solution
The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
PMID:10410796
solution sedimentati
Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
density sedimentation
PSI-MI
MI:0029
cosedimentation through density gradient
Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
PMID:10410796
density sedimentation
Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
crosslink
PSI-MI
MI:0030
cross-linking study
Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
PMID:14755292
crosslink
Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
Label transfer techniques
Photoaffinity labelling
bifunctional agent crosslink
PSI-MI
MI:0031
protein cross-linking with a bifunctional reagent
Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
PMID:10679368
PMID:7708014
Label transfer techniques
Photoaffinity labelling
bifunctional agent crosslink
The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
de novo protein sequence
PSI-MI
MS/MS
MI:0032
de novo protein sequencing by mass spectrometry
The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
PMID:10984529
de novo protein sequence
In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
PSI-MI
MI:0033
deletion analysis
In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
PMID:14755292
All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
PSI-MI
MI:0034
display technology
All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
PMID:14755292
Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
PSI-MI
MI:0035
docking
Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
PMID:11478868
PMID:9631301
The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
Rosetta Stone
PSI-MI
MI:0036
domain fusion
The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
PMID:10573422
Rosetta Stone
This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
PSI-MI
MI:0037
domain profile pairs
This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
PMID:11473021
In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
dls
PSI-MI
MI:0038
dynamic light scattering
In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
PMID:9013660
dls
In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
PSI-MI
MI:0039
edman degradation
In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
PMID:14755292
Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
Electron cryomicroscopy
Electron crystallography
PSI-MI
MI:0040
electron microscopy
Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
PMID:11785754
Electron cryomicroscopy
Electron crystallography
A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
ENDOR
endor
PSI-MI
MI:0041
electron nuclear double resonance
A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
PMID:11817959
PMID:11988476
PMID:12186859
ENDOR
endor
EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
EPR
ESR
epr
PSI-MI
MI:0042
electron paramagnetic resonance
EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
PMID:11817959
EPR
ESR
epr
A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
PSI-MI
MI:0043
electron resonance
A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
PMID:14755292
Methods based on laboratory experiments to determine an interaction.
experimental interac
PSI-MI
MI:0045
experimental interaction detection
experimental interac
Methods based on laboratory experiments to determine an interaction.
PMID:14755292
Predictive algorithms that rely on the information obtained by experimental results.
experimental info
PSI-MI
MI:0046
experimental knowledge based
Predictive algorithms that rely on the information obtained by experimental results.
PMID:14755292
experimental info
Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
Affinity blotting
PSI-MI
MI:0047
far western blotting
Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
PMID:7708014
Affinity blotting
Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
filamentous phage
PSI-MI
MI:0048
filamentous phage display
Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
PMID:7682645
filamentous phage
A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
Filter overlay assay
PSI-MI
dot blot
MI:0049
filter binding
A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
PMID:7708014
Filter overlay assay
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
flag tag coip
PSI-MI
MI:0050
flag tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
flag tag coip
Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
fluorescence
PSI-MI
MI:0051
fluorescence technology
Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
PMID:14755292
fluorescence
FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
FCS
fcs
PSI-MI
fluctuation correlation specctrometry
MI:0052
fluorescence correlation spectroscopy
FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
PMID:10733953
FCS
fcs
Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
FPS
Fluorescence anisotropy
fps
PSI-MI
MI:0053
fluorescence polarization spectroscopy
Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
PMID:12805227
PMID:7708014
FPS
Fluorescence anisotropy
fps
Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
FACS
Flow cytometry
facs
PSI-MI
MI:0054
fluorescence-activated cell sorting
Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
PMID:11988464
FACS
Flow cytometry
facs
FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
FRET
FRET analysis
RET
fret
PSI-MI
MI:0055
fluorescent resonance energy transfer
FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
PMID:11558993
FRET
FRET analysis
RET
fret
Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
full dna sequence
PSI-MI
MI:0056
full identification by DNA sequencing
Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
PMID:14755292
full dna sequence
Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
PSI-MI
MI:0057
gene neighbourhood
Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
PMID:9787636
Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
genome prediction
PSI-MI
MI:0058
genome based prediction
Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
PMID:14755292
genome prediction
The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.
OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
PSI-MI
MI:0059
gst pull down
true
The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.
OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
PMID:14755292
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.
OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
ha tag coip
PSI-MI
MI:0060
ha tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.
OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
ha tag coip
The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.
OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
PSI-MI
MI:0061
his pull down
true
The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.
OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
PMID:14755292
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
his tag coip
PSI-MI
MI:0062
his tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
his tag coip
Computational methods to predict an interaction.
in silico methods
predicted interac
PSI-MI
MI:0063
interaction prediction
Computational methods to predict an interaction.
PMID:14755292
in silico methods
predicted interac
Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
Homology based interaction prediction
PSI-MI
MI:0064
interologs mapping
Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
PMID:11731503
Homology based interaction prediction
Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
ITC
itc
PSI-MI
MI:0065
isothermal titration calorimetry
Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
PMID:11785756
ITC
itc
Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
lambda phage
PSI-MI
MI:0066
lambda phage display
Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
PMID:7682645
lambda phage
Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
PSI-MI
MI:0067
light scattering
Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
PMID:9013660
Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
modified residue ms
PSI-MI
MI:0068
mass detection of residue modification
Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
PMID:11395414
PMID:11875433
modified residue ms
Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
ms of complexes
PSI-MI
MI:0069
mass spectrometry studies of complexes
Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
PMID:12057199
PMID:12504676
ms of complexes
Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
PSI-MI
MI:0070
mobility shift
Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
PMID:14755292
In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
Gel Filtration
Size Exclusion Chromatography
Sizing column
PSI-MI
MI:0071
molecular sieving
In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
PMID:7708014
Gel Filtration
Size Exclusion Chromatography
Sizing column
Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
monoclonal western
PSI-MI
MI:0072
monoclonal antibody western blot
Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
PMID:14755292
monoclonal western
This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
PSI-MI
MI:0073
mrna display
This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
PMID:11551470
Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
PSI-MI
MI:0074
mutation analysis
Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
PMID:14755292
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
myc tag coip
PSI-MI
MI:0075
myc tag coimmunoprecipitation
true
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
PMID:14755292
myc tag coip
Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
interface predictor
PSI-MI
MI:0076
neural network on interface properties
Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
PMID:11455607
PMID:11874449
interface predictor
Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
NMR
nmr
PSI-MI
MI:0077
nuclear magnetic resonance
Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
PMID:12062432
PMID:12120505
NMR
nmr
Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
nucleotide sequence
sequence cloning
PSI-MI
MI:0078
nucleotide sequence identification
Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
PMID:14755292
nucleotide sequence
sequence cloning
Experimental methods that could not be assigned to the other large group of technologies.
OBSOLETE use biochemical (MI:0401) instead.
other biochemic tech
PSI-MI
MI:0079
other biochemical technologies
true
Experimental methods that could not be assigned to the other large group of technologies.
OBSOLETE use biochemical (MI:0401) instead.
PMID:14755292
other biochemic tech
Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
partial dna sequence hybrid
PSI-MI
MI:0080
partial DNA sequence identification by hybridization
Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
PMID:14755292
partial dna sequence hybrid
The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
PSI-MI
MI:0081
peptide array
The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
PMID:11167074
This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
fingerprinting
PSI-MI
MI:0082
peptide massfingerprinting
This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
PMID:10967324
PMID:11752590
PMID:11805826
fingerprinting
When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
PSI-MI
MI:0083
peptide synthesis
When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
PMID:14755292
Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
PSI-MI
MI:0084
phage display
Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
PMID:10975452
PMID:7708014
The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
PSI-MI
MI:0085
phylogenetic profile
The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
PMID:10200254
Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
polyclonal western
PSI-MI
MI:0086
polyclonal antibody western blot
Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
PMID:14755292
polyclonal western
Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
predictive tm
PSI-MI
MI:0087
predictive text mining
Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
PMID:11791231
predictive tm
Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
PSI-MI
MI:0088
primer specific pcr
Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
PMID:14755292
The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
PSI-MI
MI:0089
protein array
The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
PMID:10976071
PMID:12067604
In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
PCA
complementation
PSI-MI
MI:0090
protein complementation assay
In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
PMID:11495741
PCA
complementation
Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
chromatography
column chromatography
PSI-MI
MI:0091
chromatography technology
Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
PMID:14755292
chromatography
column chromatography
Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
PISA
pisa
PSI-MI
MI:0092
protein in situ array
Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
PMID:11470888
PISA
pisa
Single amino acid identification along a protein sequence.
protein sequence
PSI-MI
MI:0093
protein sequence identification
Single amino acid identification along a protein sequence.
PMID:14755292
protein sequence
A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
PSI-MI
MI:0094
protein staining
A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
PMID:12015990
ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
SELDI ProteinChip
seldi chip
PSI-MI
MI:0095
proteinchip(r) on a surface-enhanced laser desorption/ionization
ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
PMID:11827829
SELDI ProteinChip
seldi chip
A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
PSI-MI
affinity capture
pulldown
MI:0096
pull down
A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
PMID:14755292
In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
reverse RRS
reverse rrs
PSI-MI
MI:0097
reverse ras recruitment system
In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
PMID:11160938
reverse RRS
reverse rrs
This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
PSI-MI
MI:0098
ribosome display
This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
PMID:11551470
PMID:12167034
SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
RIA Radio Immuno Assay
SPA
spa
PSI-MI
MI:0099
scintillation proximity assay
SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
PMID:3866247
RIA Radio Immuno Assay
SPA
spa
Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
sequence phylogeny
PSI-MI
MI:0100
sequence based phylogenetic profile
Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
PMID:11707606
sequence phylogeny
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
predict from sequenc
PSI-MI
MI:0101
sequence based prediction
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
PMID:14755292
predict from sequenc
This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
sequence tag
PSI-MI
MS/MS
MI:0102
sequence tag identification
This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
PMID:10967324
PMID:11752590
PMID:11805837
sequence tag
A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
PSI-MI
MI:0103
southern blot
A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
PMID:14755292
In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
sls
PSI-MI
MI:0104
static light scattering
In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
PMID:9013660
sls
Methods based on 3D structure information.
predict from struct
PSI-MI
MI:0105
structure based prediction
Methods based on 3D structure information.
PMID:14755292
predict from struct
Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
PSI-MI
MI:0106
surface patches
Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
PMID:9299343
This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
BIAcore(r)
Optical biosensor
spr
PSI-MI
MI:0107
surface plasmon resonance
This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
PMID:11896282
PMID:12120258
PMID:16338355
BIAcore(r)
Optical biosensor
spr
T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
t7 phage
PSI-MI
MI:0108
Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1.
t7 phage display
T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
PMID:14755292
t7 phage
The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).
OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
tap tag coip
PSI-MI
MI:0109
tap tag coimmunoprecipitation
true
The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).
OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
PMID:10504710
tap tag coip
Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
PSI-MI
MI:0110
text mining
Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
PMID:14755292
The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
dhfr reconstruction
PSI-MI
MI:0111
dihydrofolate reductase reconstruction
The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
PMID:10318894
dhfr reconstruction
The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
ub reconstruction
PSI-MI
membrane yeast two-hybrid
myth
split-ubiquitin
MI:0112
ubiquitin reconstruction
The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
PMID:9560251
ub reconstruction
Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
Immuno blot
PSI-MI
MI:0113
western blot
Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
PMID:14755292
Immuno blot
Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
X-ray
x-ray diffraction
PSI-MI
co-crystallization
co-crystallography
MI:0114
x-ray crystallography
Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
PMID:14755292
X-ray
x-ray diffraction
The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
PSI-MI
MI:0115
yeast display
The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
PMID:9181578
Property of a subsequence that may interfere with the binding of a molecule.
PSI-MI
MI:0116
feature type
Property of a subsequence that may interfere with the binding of a molecule.
PMID:14755292
A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
binding site
binding region
PSI-MI
binding component
MI:0117
binding-associated region
A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
PMID:14755292
binding region
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
PSI-MI
MI:0118
mutation
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
PMID:14755292
Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
hotspot
mutation decreasing
PSI-MI
MI:0119
mutation decreasing interaction
Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
PMID:14755292
hotspot
mutation decreasing
Residue covalent modifications occurring in the specific protein form involved in an interaction.
OBSOLETE remap to MOD:00000.
ptm
PSI-MI
MI:0120
post translation modification
true
Residue covalent modifications occurring in the specific protein form involved in an interaction.
OBSOLETE remap to MOD:00000.
PMID:14755292
ptm
Residue modification.
OBSOLETE remap to MOD:00394.
PSI-MI
MI:0121
acetylated residue
true
Residue modification.
OBSOLETE remap to MOD:00394.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00050.
(S)-2-(acetylamino)propanoic acid
AAC
N-acetyl-L-alanine
[A:ac]
acetylalanine
PSI-MI
MI:0122
n-acetyl-alanine
true
Residue modification.
OBSOLETE remap to MOD:00050.
PMID:11125103
RESID:AA0041
(S)-2-(acetylamino)propanoic acid
AAC
N-acetyl-L-alanine
[A:ac]
acetylalanine
acetylalanine
Residue modification.
OBSOLETE remap to MOD:00359.
N2-acetyl-L-arginine
RAC
[R:ac]
acetylarginine
alpha-acetylamino-delta-guanidinovaleric acid
PSI-MI
MI:0123
n2-acetyl-arginine
true
Residue modification.
OBSOLETE remap to MOD:00359.
PMID:11125103
RESID:AA0354
N2-acetyl-L-arginine
RAC
[R:ac]
acetylarginine
acetylarginine
alpha-acetylamino-delta-guanidinovaleric acid
Residue modification.
OBSOLETE remap to MOD:00780.
N-acetyl-L-asparagine
NAC
[N:ac]
acetylasparagine
PSI-MI
MI:0124
n-acetyl-asparagine
true
Residue modification.
OBSOLETE remap to MOD:00780.
PMID:11125103
N-acetyl-L-asparagine
NAC
[N:ac]
acetylasparagine
Residue modification.
OBSOLETE remap to MOD:00051.
(S)-2-(acetylamino)butanedioic acid
DAC
N-acetyl-L-aspartic acid
[D:ac]
acetylaspartate
acetylaspartic acid
PSI-MI
MI:0125
n-acetyl-aspartic acid
true
Residue modification.
OBSOLETE remap to MOD:00051.
PMID:11125103
RESID:AA0042
(S)-2-(acetylamino)butanedioic acid
DAC
N-acetyl-L-aspartic acid
[D:ac]
acetylaspartate
acetylaspartic acid
Residue modification.
OBSOLETE remap to MOD:00052.
(R)-2-acetylamino-3-sulfanylpropanoic acid
2-acetylamino-3-mercaptopropanoic acid
CAC
N-acetyl-L-cysteine
N-acetylcysteine
[C:ac]
acetylcysteine
PSI-MI
MI:0126
n-acetyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00052.
PMID:11125103
RESID:AA0043
(R)-2-acetylamino-3-sulfanylpropanoic acid
2-acetylamino-3-mercaptopropanoic acid
CAC
N-acetyl-L-cysteine
N-acetylcysteine
[C:ac]
acetylcysteine
Residue modification.
OBSOLETE remap to MOD:00054.
(S)-2-acetylamino-5-pentanediamic acid
N-acetyl-L-glutamine
QAC
[Q:ac]
acetylglutamine
PSI-MI
MI:0127
n-acetyl-glutamine
true
Residue modification.
OBSOLETE remap to MOD:00054.
PMID:11125103
RESID:AA0045
(S)-2-acetylamino-5-pentanediamic acid
N-acetyl-L-glutamine
QAC
[Q:ac]
acetylglutamine
acetylglutamine
Residue modification.
OBSOLETE remap to MOD:00053.
(S)-2-(acetylamino)pentanedioic acid
EAC
N-acetyl-L-glutamic acid
[E:ac]
acetylglutamate
acetylglutamic acid
PSI-MI
MI:0128
n-acetyl-glutamic acid
true
Residue modification.
OBSOLETE remap to MOD:00053.
PMID:11125103
RESID:AA0044
(S)-2-(acetylamino)pentanedioic acid
EAC
N-acetyl-L-glutamic acid
[E:ac]
acetylglutamate
acetylglutamic acid
Residue modification.
OBSOLETE remap to MOD:00055.
2-(acetylamino)ethanoic acid
GAC
N-acetylglycine
[G:ac]
aceturic acid
acetylglycine
PSI-MI
MI:0129
n-acetylglycine
true
Residue modification.
OBSOLETE remap to MOD:00055.
PMID:11125103
RESID:AA0046
2-(acetylamino)ethanoic acid
GAC
N-acetylglycine
[G:ac]
aceturic acid
acetylglycine
Residue modification.
OBSOLETE remap to MOD:00781.
HAC
N-acetyl-L-histidine
[H:ac]
acetylhistidine
PSI-MI
MI:0130
n-acetyl-histidine
true
Residue modification.
OBSOLETE remap to MOD:00781.
PMID:11125103
HAC
N-acetyl-L-histidine
[H:ac]
acetylhistidine
Residue modification.
OBSOLETE remap to MOD:00056.
(2S,3S)-2-acetylamino-3-methylpentanoic acid
IAC
N-acetyl-L-isoleucine
[I:ac]
acetylisoleucine
PSI-MI
MI:0131
n-acetyl-isoleucine
true
Residue modification.
OBSOLETE remap to MOD:00056.
PMID:11125103
RESID:AA0047
(2S,3S)-2-acetylamino-3-methylpentanoic acid
IAC
N-acetyl-L-isoleucine
[I:ac]
acetylisoleucine
acetylisoleucine
Residue modification.
OBSOLETE remap to MOD:00782.
LAC
N-acetyl-L-leucine
[L:ac]
acetylleucine
PSI-MI
MI:0132
n-acetyl-leucine
true
Residue modification.
OBSOLETE remap to MOD:00782.
PMID:11125103
LAC
N-acetyl-L-leucine
[L:ac]
acetylleucine
Residue modification.
OBSOLETE remap to MOD:00057.
(S)-2-acetylamino-6-aminohexanoic acid
KAC
N2-acetyl-L-lysine
N2-acetyllysine
[K:ac]
n2-acetyllysine
PSI-MI
MI:0133
n2-acetyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00057.
PMID:11125103
RESID:AA0048
(S)-2-acetylamino-6-aminohexanoic acid
KAC
N2-acetyl-L-lysine
N2-acetyllysine
[K:ac]
n2-acetyllysine
Residue modification.
OBSOLETE remap to MOD:00064.
(S)-2-amino-6-(acetylamino)hexanoic acid
KA6
N(zeta)-acetyllysine
N6-acetyl-L-lysine
[K:N6ac]
epsilon-acetyllysine
n6-acetyllysine
PSI-MI
MI:0134
n6-acetyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00064.
PMID:11125103
RESID:AA0055
(S)-2-amino-6-(acetylamino)hexanoic acid
KA6
N(zeta)-acetyllysine
N6-acetyl-L-lysine
[K:N6ac]
epsilon-acetyllysine
n6-acetyllysine
Residue modification.
OBSOLETE remap to MOD:00058.
(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
2-acetylamino-4-(methylthio)butanoic acid
MAC
N-acetyl-L-methionine
[M:ac]
acetylmethionine
methionamine
PSI-MI
MI:0135
n-acetyl-methionine
true
Residue modification.
OBSOLETE remap to MOD:00058.
PMID:11125103
RESID:AA0049
(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
2-acetylamino-4-(methylthio)butanoic acid
MAC
N-acetyl-L-methionine
[M:ac]
acetylmethionine
acetylmethionine
methionamine
Residue modification.
OBSOLETE remap to MOD:00784.
FAC
N-acetyl-L-phenylalanine
[F:ac]
acetylphenylalanine
PSI-MI
MI:0136
n-acetyl-phenylalanine
true
Residue modification.
OBSOLETE remap to MOD:00784.
PMID:11125103
FAC
N-acetyl-L-phenylalanine
[F:ac]
acetylphenylalanine
Residue modification.
OBSOLETE remap to MOD:00059.
(2S)-1-acetyl-2-pyrrolidinecarboxylic acid
N-acetyl-L-proline
PAC
[P:ac]
acetylproline
PSI-MI
MI:0137
n-acetyl-proline
true
Residue modification.
OBSOLETE remap to MOD:00059.
PMID:11125103
RESID:AA0050
(2S)-1-acetyl-2-pyrrolidinecarboxylic acid
N-acetyl-L-proline
PAC
[P:ac]
acetylproline
acetylproline
Residue modification.
OBSOLETE remap to MOD:00060.
(S)-2-acetylamino-3-hydroxypropanoic acid
N-acetyl-L-serine
N-acetylserine
SAC
[S:ac]
acetylserine
PSI-MI
MI:0138
n-acetyl-serine
true
Residue modification.
OBSOLETE remap to MOD:00060.
PMID:11125103
RESID:AA0051
(S)-2-acetylamino-3-hydroxypropanoic acid
N-acetyl-L-serine
N-acetylserine
SAC
[S:ac]
acetylserine
Residue modification.
OBSOLETE remap to MOD:00061.
(2S,3R)-2-acetylamino-3-hydroxybutanoic acid
N-acetyl-L-threonine
N-acetylthreonine
TAC
[T:ac]
acetylthreonine
PSI-MI
MI:0139
n-acetyl-threonine
true
Residue modification.
OBSOLETE remap to MOD:00061.
PMID:11125103
RESID:AA0052
(2S,3R)-2-acetylamino-3-hydroxybutanoic acid
N-acetyl-L-threonine
N-acetylthreonine
TAC
[T:ac]
acetylthreonine
Residue modification.
OBSOLETE remap to MOD:00785.
N-acetyl-L-tryptophan
WAC
[W:ac]
acetyltryptophan
PSI-MI
MI:0140
n-acetyl-tryptophan
true
Residue modification.
OBSOLETE remap to MOD:00785.
PMID:11125103
N-acetyl-L-tryptophan
WAC
[W:ac]
acetyltryptophan
Residue modification.
OBSOLETE remap to MOD:00062.
(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
N-acetyl-L-tyrosine
N-acetyltyrosine
YAC
[Y:ac]
acetyltyrosine
PSI-MI
MI:0141
n-acetyl-tyrosine
true
Residue modification.
OBSOLETE remap to MOD:00062.
PMID:11125103
RESID:AA0053
(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
N-acetyl-L-tyrosine
N-acetyltyrosine
YAC
[Y:ac]
acetyltyrosine
Residue modification.
OBSOLETE remap to MOD:00063.
(S)-2-acetylamino-3-methylbutanoic acid
N-acetyl-L-valine
N-acetylvaline
VAC
[V:ac]
acetylvaline
PSI-MI
MI:0142
n-acetyl-valine
true
Residue modification.
OBSOLETE remap to MOD:00063.
PMID:11125103
RESID:AA0054
(S)-2-acetylamino-3-methylbutanoic acid
N-acetyl-L-valine
N-acetylvaline
VAC
[V:ac]
acetylvaline
Residue modification.
OBSOLETE remap to MOD:00674.
PSI-MI
MI:0143
amidated residue
true
Residue modification.
OBSOLETE remap to MOD:00674.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00091.
(S)-2-amino-5-guanidinopentanamide
L-arginine amide
RAM
[R:am]
argininamide
arginineamide
PSI-MI
MI:0145
arginine amide
true
Residue modification.
OBSOLETE remap to MOD:00091.
PMID:11125103
RESID:AA0082
(S)-2-amino-5-guanidinopentanamide
L-arginine amide
RAM
[R:am]
argininamide
arginineamide
Residue modification.
OBSOLETE remap to MOD:00493.
PSI-MI
MI:0146
formylated residue
true
Residue modification.
OBSOLETE remap to MOD:00493.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00030.
(S)-2-formylamino-4-(methylsulfanyl)butanoic acid
2-formylamino-4-(methylthio)butanoic acid
MFM
N-formyl-L-methionine
[M:form]
formylmethionine
PSI-MI
MI:0147
n-formyl-methionine
true
Residue modification.
OBSOLETE remap to MOD:00030.
PMID:11125103
RESID:AA0021
(S)-2-formylamino-4-(methylsulfanyl)butanoic acid
2-formylamino-4-(methylthio)butanoic acid
MFM
N-formyl-L-methionine
[M:form]
formylmethionine
Residue modification.
OBSOLETE remap to MOD:00428.
PSI-MI
MI:0148
hydroxylated residue
true
Residue modification.
OBSOLETE remap to MOD:00428.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:01155.
PSI-MI
MI:0150
lipid modification
true
Residue modification.
OBSOLETE remap to MOD:01155.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00111.
(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
CFN
S-farnesyl-L-cysteine
[C:farn]
farnesylcysteine
PSI-MI
MI:0151
s-farnesyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00111.
PMID:11125103
RESID:AA0102
(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
CFN
S-farnesyl-L-cysteine
[C:farn]
farnesylcysteine
Residue modification.
OBSOLETE remap to MOD:00113.
(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
CGR
S-geranylgeranyl-L-cysteine
[C:ger]
geranylgeranylcys
PSI-MI
MI:0152
s-geranylgeranyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00113.
PMID:11125103
RESID:AA0104
(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
CGR
S-geranylgeranyl-L-cysteine
[C:ger]
geranylgeranylcys
Residue modification.
OBSOLETE remap to MOD:00069.
(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
2-hexadecanoylamino-3-mercaptopropanoic acid
CPN
N-(1-oxahexadecyl)-L-cysteine
N-palmitoyl-L-cysteine
[C:palm_n]
n-palmitoylcysteine
PSI-MI
MI:0153
n-palmitoyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00069.
PMID:11125103
RESID:AA0060
(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
2-hexadecanoylamino-3-mercaptopropanoic acid
CPN
N-(1-oxahexadecyl)-L-cysteine
N-palmitoyl-L-cysteine
[C:palm_n]
n-palmitoylcysteine
Residue modification.
OBSOLETE remap to MOD:00115.
(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
2-amino-3-(hexadecanoylthio)propanoic acid
CPS
S-palmitoyl-L-cysteine
[C:palm_s]
cysteine hexadecanoate thioester
cysteine palmitate thioester
s-palmitoylcysteine
PSI-MI
MI:0154
s-palmitoyl-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00115.
PMID:11125103
RESID:AA0106
(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
2-amino-3-(hexadecanoylthio)propanoic acid
CPS
S-palmitoyl-L-cysteine
[C:palm_s]
cysteine hexadecanoate thioester
cysteine palmitate thioester
s-palmitoylcysteine
Residue modification.
OBSOLETE remap to MOD:00068.
GMY
N-myristoyl-glycine
[G:myr]
myristoylglycine
PSI-MI
MI:0155
n-myristoyl-glycine
true
Residue modification.
OBSOLETE remap to MOD:00068.
PMID:11125103
RESID:AA0059
GMY
N-myristoyl-glycine
[G:myr]
myristoylglycine
Residue modification.
OBSOLETE remap to MOD:00087.
(S)-2-amino-6-(tetradecanoylamino)hexanoic acid
KMY
N(zeta)-myristoyllysine
N6-(1-oxotetradecyl)-L-lysine
N6-myristoyl-L-lysine
[K:myr]
epsilon-myristoyllysine
myristoyllysine
PSI-MI
MI:0156
n6-myristoyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00087.
PMID:11125103
RESID:AA0078
(S)-2-amino-6-(tetradecanoylamino)hexanoic acid
KMY
N(zeta)-myristoyllysine
N6-(1-oxotetradecyl)-L-lysine
N6-myristoyl-L-lysine
[K:myr]
epsilon-myristoyllysine
myristoyllysine
Residue modification.
OBSOLETE remap to MOD:00427.
PSI-MI
MI:0157
methylated residue
true
Residue modification.
OBSOLETE remap to MOD:00427.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00070.
(S)-2-methylaminopropanoic acid
AMT
N-methyl-L-alanine
N-methylalanine
[A:meth_n]
methylalanine
PSI-MI
MI:0158
n-methyl-alanine
true
Residue modification.
OBSOLETE remap to MOD:00070.
PMID:11125103
RESID:AA0061
(S)-2-methylaminopropanoic acid
AMT
N-methyl-L-alanine
N-methylalanine
[A:meth_n]
methylalanine
Residue modification.
OBSOLETE remap to MOD:00071.
(S)-1-carboxy-N,N,N-trimethylethanaminium
(S)-2-(trimethylammonio)propanoic acid
AM3
N,N,N-trimethyl-L-alanine
[A:meth_n3]
trimethylalanine
PSI-MI
MI:0159
n,n,n-trimethyl-alanine
true
Residue modification.
OBSOLETE remap to MOD:00071.
PMID:11125103
RESID:AA0062
(S)-1-carboxy-N,N,N-trimethylethanaminium
(S)-2-(trimethylammonio)propanoic acid
AM3
N,N,N-trimethyl-L-alanine
[A:meth_n3]
trimethylalanine
Residue modification.
OBSOLETE remap to MOD:00077.
(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
NG,NG-dimethylarginine
RM2
[R:meth_n7]
asymmetric dimethylarginine
dimethylarginine
omega-N,omega-N-dimethyl-L-arginine
PSI-MI
MI:0160
omega-n,omega-n-dimethyl-arginine
true
Residue modification.
OBSOLETE remap to MOD:00077.
PMID:11125103
RESID:AA0068
(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
NG,NG-dimethylarginine
RM2
[R:meth_n7]
asymmetric dimethylarginine
dimethylarginine
omega-N,omega-N-dimethyl-L-arginine
Residue modification.
OBSOLETE remap to MOD:00237.
(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
3-carboxy-S-methyl-cysteine
3-methylthio-aspartic acid
DM2
L-beta-methylthioaspartic acid
[D:meth_b]
beta-methylthio-aspartic acid
methylthioaspartate
PSI-MI
MI:0161
beta-methylthioaspartic acid
true
Residue modification.
OBSOLETE remap to MOD:00237.
PMID:11125103
RESID:AA0232
(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
3-carboxy-S-methyl-cysteine
3-methylthio-aspartic acid
DM2
L-beta-methylthioaspartic acid
[D:meth_b]
beta-methylthio-aspartic acid
methylthioaspartate
Residue modification.
OBSOLETE remap to MOD:00080.
(S)-2-amino-N5-methylpentanediamic acid
N(delta)-methylglutamine
N-methylglutamine
N5-methyl-L-glutamine
QM5
[Q:meth_n5]
gamma-methylglutamine
methylglutamine
PSI-MI
MI:0162
n5-methyl-glutamine
true
Residue modification.
OBSOLETE remap to MOD:00080.
PMID:11125103
RESID:AA0071
(S)-2-amino-N5-methylpentanediamic acid
N(delta)-methylglutamine
N-methylglutamine
N5-methyl-L-glutamine
QM5
[Q:meth_n5]
gamma-methylglutamine
methylglutamine
Residue modification.
OBSOLETE remap to MOD:00081.
(S)-2-aminopentanedioic acid 5-methyl ester
5-methyl-L-glutamate
EM5
L-glutamic acid 5-methyl ester
[E:meth_o5]
glutamatemethylester
glutamic acid gamma-methyl ester
PSI-MI
MI:0163
glutamic acid 5-methyl ester
true
Residue modification.
OBSOLETE remap to MOD:00081.
PMID:11125103
RESID:AA0072
(S)-2-aminopentanedioic acid 5-methyl ester
5-methyl-L-glutamate
EM5
L-glutamic acid 5-methyl ester
[E:meth_o5]
glutamatemethylester
glutamic acid gamma-methyl ester
Residue modification.
OBSOLETE remap to MOD:00085.
(S)-2-amino-6-methylaminohexanoic acid
MLZ
N(zeta)-methyllysine
N6-methyl-L-lysine
[K:meth_1]
epsilon-methyllysine
methyllysine
PSI-MI
MI:0165
n6-methyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00085.
PMID:11125103
(S)-2-amino-6-methylaminohexanoic acid
MLZ
N(zeta)-methyllysine
N6-methyl-L-lysine
[K:meth_1]
epsilon-methyllysine
methyllysine
Residue modification.
OBSOLETE remap to MOD:00084.
(S)-2-amino-6-dimethylaminohexanoic acid
MLY
N(zeta)-dimethyllysine
N6,N6-dimethyl-L-lysine
[K:meth_2]
dimethyllysine
epsilon-dimethyllysine
lysine derivative Lys(y)
PSI-MI
MI:0166
n6,n6-dimethyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00084.
PMID:11125103
RESID:AA0075
(S)-2-amino-6-dimethylaminohexanoic acid
MLY
N(zeta)-dimethyllysine
N6,N6-dimethyl-L-lysine
[K:meth_2]
dimethyllysine
epsilon-dimethyllysine
lysine derivative Lys(y)
Residue modification.
OBSOLETE remap to MOD:00083.
(S)-2-amino-6-(trimethylammonio)hexanoic acid
(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium
M3L
N(zeta)-trimethyllysine
N6,N6,N6-trimethyl-L-lysine
[K:meth_3]
epsilon-trimethyllysine
trimethyllysine
PSI-MI
MI:0167
n6,n6,n6-trimethyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00083.
PMID:11125103
RESID:AA0074
(S)-2-amino-6-(trimethylammonio)hexanoic acid
(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium
M3L
N(zeta)-trimethyllysine
N6,N6,N6-trimethyl-L-lysine
[K:meth_3]
epsilon-trimethyllysine
trimethyllysine
Residue modification.
OBSOLETE remap to MOD:00073.
(S)-2-methylamino-4-(methylsulfanyl)butanoic acid
2-methylamino-4-(methylthio)butanoic acid
MMT
N-methyl-L-methionine
N-methylmethionine
[M:meth]
methylmethionine
PSI-MI
MI:0168
n-methyl-methionine
true
Residue modification.
OBSOLETE remap to MOD:00073.
PMID:11125103
RESID:AA0064
(S)-2-methylamino-4-(methylsulfanyl)butanoic acid
2-methylamino-4-(methylthio)butanoic acid
MMT
N-methyl-L-methionine
N-methylmethionine
[M:meth]
methylmethionine
Residue modification.
OBSOLETE remap to MOD:00074.
(S)-2-methylamino-3-phenylpropanoic acid
FMT
N-methyl-L-phenylalanine
N-methylphenylalanine
[F:meth]
methylphenylalanine
PSI-MI
MI:0169
n-methyl-phenylalanine
true
Residue modification.
OBSOLETE remap to MOD:00074.
PMID:14755292
(S)-2-methylamino-3-phenylpropanoic acid
FMT
N-methyl-L-phenylalanine
N-methylphenylalanine
[F:meth]
methylphenylalanine
Residue modification.
OBSOLETE remap to MOD:00696.
phosphorylated
PSI-MI
MI:0170
phosphorylated residue
true
Residue modification.
OBSOLETE remap to MOD:00696.
PMID:11125103
phosphorylated
Residue modification.
OBSOLETE remap to MOD:00227.
(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
N5-[imino(phosphonoamino)methyl]-L-ornithine
RPO
[R:po]
alpha-amino-delta-phosphonoguanidinovaleric acid
omega-N-phospho-L-arginine
phosphoarginine
PSI-MI
MI:0171
omega-n-phospho-arginine
true
Residue modification.
OBSOLETE remap to MOD:00227.
PMID:11125103
RESID:AA0222
(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
N5-[imino(phosphonoamino)methyl]-L-ornithine
RPO
[R:po]
alpha-amino-delta-phosphonoguanidinovaleric acid
omega-N-phospho-L-arginine
phosphoarginine
Residue modification.
OBSOLETE remap to MOD:00042.
(S)-2-aminobutanedioic 4-phosphoric anhydride
DPO
L-aspartic 4-phosphoric anhydride
[D:po]
beta-aspartyl phosphate
phosphoaspartic acid
PSI-MI
MI:0172
aspartic 4-phosphoric anhydride
true
Residue modification.
OBSOLETE remap to MOD:00042.
PMID:11125103
RESID:AA0033
(S)-2-aminobutanedioic 4-phosphoric anhydride
DPO
L-aspartic 4-phosphoric anhydride
[D:po]
beta-aspartyl phosphate
phosphoaspartic acid
phosphoaspartic acid
Residue modification.
OBSOLETE remap to MOD:00043.
(R)-2-amino-3-(phosphonosulfanyl)propanoic acid
CPO
S-phospho-L-cysteine
S-phosphonocysteine
S3-phosphocysteine
[C:po]
cysteine phosphate thioester
phosphocysteine
PSI-MI
MI:0173
s-phospho-cysteine
true
Residue modification.
OBSOLETE remap to MOD:00043.
PMID:11125103
RESID:AA0034
(R)-2-amino-3-(phosphonosulfanyl)propanoic acid
CPO
S-phospho-L-cysteine
S-phosphonocysteine
S3-phosphocysteine
[C:po]
cysteine phosphate thioester
phosphocysteine
Residue modification.
OBSOLETE remap to MOD:00046.
(S)-2-amino-3-(phosphonooxy)propanoic acid
2-amino-3-hydroxypropanoic acid 3-phosphate
2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
O-phospho-L-serine
O-phosphonoserine
O3-phosphoserine
SPO
[S:po]
phosphoserine
serine phosphate ester
PSI-MI
MI:0176
o-phospho-serine
true
Residue modification.
OBSOLETE remap to MOD:00046.
PMID:11125103
RESID:AA0037
(S)-2-amino-3-(phosphonooxy)propanoic acid
2-amino-3-hydroxypropanoic acid 3-phosphate
2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
O-phospho-L-serine
O-phosphonoserine
O3-phosphoserine
SPO
[S:po]
phosphoserine
serine phosphate ester
Residue modification.
OBSOLETE remap to MOD:00047.
(2S,3R)-2-amino-3-phosphonooxybutanoic acid
2-amino-3-hydroxybutanoic acid 3-phosphate
O-phospho-L-threonine
O3-phosphothreonine
TPO
[T:po]
phosphothreonine
threonine phosphate ester
PSI-MI
MI:0177
o-phospho-threonine
true
Residue modification.
OBSOLETE remap to MOD:00047.
PMID:11125103
RESID:AA0038
(2S,3R)-2-amino-3-phosphonooxybutanoic acid
2-amino-3-hydroxybutanoic acid 3-phosphate
O-phospho-L-threonine
O3-phosphothreonine
TPO
[T:po]
phosphothreonine
threonine phosphate ester
Residue modification.
OBSOLETE remap to MOD:00048.
(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
O4'-phospho-L-tyrosine
O4-phosphotyrosine
YPO
[Y:po]
phosphotyrosine
tyrosine phosphate
PSI-MI
MI:0178
o4'-phospho-tyrosine
true
Residue modification.
OBSOLETE remap to MOD:00048.
PMID:11125103
RESID:AA0039
(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
O4'-phospho-L-tyrosine
O4-phosphotyrosine
YPO
[Y:po]
phosphotyrosine
tyrosine phosphate
Residue modification.
OBSOLETE remap to MOD:00032.
PSI-MI
MI:0179
other modification
true
Residue modification.
OBSOLETE remap to MOD:00032.
PMID:11125103
Residue modification.
OBSOLETE remap to MOD:00031.
3-selenylalanine
CSE
L-selenocysteine
[C:sel]
selenium cysteine
PSI-MI
MI:0180
selenocysteine
true
Residue modification.
OBSOLETE remap to MOD:00031.
PMID:11125103
RESID:AA0022
3-selenylalanine
CSE
L-selenocysteine
[C:sel]
selenium cysteine
Residue modification.
OBSOLETE remap to MOD:00530.
L-selenomethionine
MSE
[M:sel]
PSI-MI
MI:0181
selenomethionine
true
Residue modification.
OBSOLETE remap to MOD:00530.
PMID:11125103
L-selenomethionine
MSE
[M:sel]
Residue modification.
OBSOLETE remap to MOD:01169.
(S)-2-amino-3-oxopropanoic acid
2-amino-3-oxopropionic acid
L-3-oxoalanine
L-alpha-formylglycine
L-amino-malonic acid semialdehyde
L-aminomalonaldehydic acid
L-serinesemialdehyde [misnomer]
SOX
[S:oxal]
oxoalanine
PSI-MI
MI:0182
3-oxoalanine
true
Residue modification.
OBSOLETE remap to MOD:01169.
PMID:11125103
RESID:AA0185
(S)-2-amino-3-oxopropanoic acid
2-amino-3-oxopropionic acid
L-3-oxoalanine
L-alpha-formylglycine
L-amino-malonic acid semialdehyde
L-aminomalonaldehydic acid
L-serinesemialdehyde [misnomer]
SOX
[S:oxal]
oxoalanine
Residue modification.
OBSOLETE remap to MOD:00179.
(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
EGE
L-glutamyl 5-glycerophosphoethanolamine
L-glutamyl 5-glycerophosphorylethanolamine
L-glutamyl 5-glycerylphosphorylethanolamine
[E:gpe]
glycerylpo4etohamine
PSI-MI
MI:0184
glutamyl 5-glycerylphosphorylethanolamine
true
Residue modification.
OBSOLETE remap to MOD:00179.
PMID:11125103
RESID:AA0170
(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
EGE
L-glutamyl 5-glycerophosphoethanolamine
L-glutamyl 5-glycerophosphorylethanolamine
L-glutamyl 5-glycerylphosphorylethanolamine
[E:gpe]
glycerylpo4etohamine
Residue modification.
OBSOLETE remap to MOD:00126.
(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
KBT
N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
N6-biotinyl-L-lysine
N6-biotinyllysine
[K:biotin]
biocytin
biotinyllysine
epsilon-N-biotinyllysine
PSI-MI
MI:0186
n6-biotinyl-lysine
true
Residue modification.
OBSOLETE remap to MOD:00126.
PMID:11125103
RESID:AA0117
(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
KBT
N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
N6-biotinyl-L-lysine
N6-biotinyllysine
[K:biotin]
biocytin
biotinyllysine
epsilon-N-biotinyllysine
Residue modification.
OBSOLETE remap to MOD:00125.
(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
KHY
N6-(4-amino-2-hydroxybutyl)-L-lysine
[K:hypu]
hypusine
PSI-MI
MI:0187
n6-(4-amino-2-hydroxybutyl)-lysine
true
Residue modification.
OBSOLETE remap to MOD:00125.
PMID:11125103
RESID:AA0116
(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
KHY
N6-(4-amino-2-hydroxybutyl)-L-lysine
[K:hypu]
hypusine
hypusine
Residue modification.
OBSOLETE remap to MOD:00129.
(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
KRT
N6-retinal-L-lysine
N6-retinyl-lysine
N6-retinylidene-L-lysine
[K:retin]
retinallysine
PSI-MI
MI:0188
n6-retinal-lysine
true
Residue modification.
OBSOLETE remap to MOD:00129.
PMID:11125103
RESID:AA0120
(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
KRT
N6-retinal-L-lysine
N6-retinyl-lysine
N6-retinylidene-L-lysine
[K:retin]
retinallysine
Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.
OBSOLETE remap to MOD:00134.
KUB
N6-glycyl-L-lysine
N6-glycyllysine
[K:ub]
PSI-MI
MI:0189
ubiquitinated lysine
true
Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.
OBSOLETE remap to MOD:00134.
PMID:11125103
RESID:AA0125
KUB
N6-glycyl-L-lysine
N6-glycyllysine
[K:ub]
Connection between molecule.
PSI-MI
MI:0190
interaction type
Connection between molecule.
PMID:14755292
Physical association among molecules.
OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
PSI-MI
MI:0191
aggregation
true
Physical association among molecules.
OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
PMID:14755292
Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
acetylation
PSI-MI
MI:0192
acetylation reaction
Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
GO:0006473
PMID:14755292
RESID:AA0041
RESID:AA0042
RESID:AA0043
RESID:AA0044
RESID:AA0045
RESID:AA0046
RESID:AA0047
RESID:AA0048
RESID:AA0049
RESID:AA0050
RESID:AA0051
RESID:AA0052
RESID:AA0053
RESID:AA0054
RESID:AA0055
RESID:AA0056
acetylation
Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
amidation
PSI-MI
MI:0193
amidation reaction
Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
GO:0001519
PMID:14755292
RESID:AA0081
RESID:AA0082
RESID:AA0083
RESID:AA0084
RESID:AA0085
RESID:AA0086
RESID:AA0087
RESID:AA0088
RESID:AA0089
RESID:AA0090
RESID:AA0091
RESID:AA0092
RESID:AA0093
RESID:AA0094
RESID:AA0095
RESID:AA0096
RESID:AA0097
RESID:AA0098
RESID:AA0099
RESID:AA0100
amidation
Covalent bond breakage in a molecule leading to the formation of smaller molecules.
cleavage
PSI-MI
MI:0194
cleavage reaction
Covalent bond breakage in a molecule leading to the formation of smaller molecules.
PMID:14755292
cleavage
Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
PSI-MI
MI:0195
covalent binding
Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
PMID:14755292
Physical interaction mediated by covalent bond rearrangement.
OBSOLETE use covalent binding (MI:0195) instead.
PSI-MI
MI:0196
covalent interaction
true
Physical interaction mediated by covalent bond rearrangement.
OBSOLETE use covalent binding (MI:0195) instead.
PMID:14755292
N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
deacetylation
PSI-MI
MI:0197
deacetylation reaction
N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
GO:0006476
PMID:14755292
RESID:AA0055
RESID:AA0056
deacetylation
S-farnesyl-L-cysteined is cleaved and returns a C residue.
defarnesylation
PSI-MI
MI:0198
defarnesylation reaction
S-farnesyl-L-cysteined is cleaved and returns a C residue.
PMID:14755292
RESID:AA0102
defarnesylation
N6-formyl-L-lysine is cleaved and returns a K residue.
deformylation
PSI-MI
MI:0199
deformylation reaction
N6-formyl-L-lysine is cleaved and returns a K residue.
PMID:14755292
RESID:AA0211
deformylation
S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
degeranylation
PSI-MI
MI:0200
degeranylation reaction
S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
PMID:14755292
RESID:AA0104
degeranylation
N6-myristoyl-L-lysine is cleaved and returns a K residue.
demyristoylation
PSI-MI
MI:0201
demyristoylation reaction
N6-myristoyl-L-lysine is cleaved and returns a K residue.
PMID:14755292
RESID:AA0078
demyristoylation
S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
depalmitoylation
PSI-MI
MI:0202
depalmitoylation reaction
S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
PMID:14755292
RESID:AA0060
RESID:AA0077
RESID:AA0106
depalmitoylation
Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
dephosphorylation
PSI-MI
MI:0203
dephosphorylation reaction
Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
GO:0016311
PMID:14755292
RESID:AA0033
RESID:AA0034
RESID:AA0035
RESID:AA0036
RESID:AA0037
RESID:AA0038
RESID:AA0039
RESID:AA0222
dephosphorylation
Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
deubiquitination
PSI-MI
MI:0204
deubiquitination reaction
Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
GO:0016579
PMID:11583613
RESID:AA0125
deubiquitination
Dissociation of partners interacting via non-covalent bond.
OBSOLETE because considered misleading.
PSI-MI
MI:0205
disaggregation
true
Dissociation of partners interacting via non-covalent bond.
OBSOLETE because considered misleading.
PMID:14755292
Reversible reaction that can affect C residue.
farnesylation
PSI-MI
MI:0206
farnesylation reaction
Reversible reaction that can affect C residue.
GO:0018347
PMID:14755292
RESID:AA0102
farnesylation
Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
formylation
PSI-MI
MI:0207
formylation reaction
Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
GO:0018256
PMID:14755292
RESID:AA0057
RESID:AA0211
formylation
An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E
A genetic interaction refers to an unexpected phenotype not easily explained by combining the effects of individual genetic variants (7).
A quantitative genetic interaction definition has two components: a quantitative phenotypic measure and a neutrality function that predicts the phenotype of an organism carrying two noninteracting mutations. Interaction is then defined by deviation of a double-mutant organism's phenotype from the expected neutral phenotype.
More generally, a genetic interaction can be defined as the difference between an experimentally measured double-mutant phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the mutations act independently.
Two genes A and B 'genetically interact' when the phenotype generated as the result of mutations in both genes (double mutant ab) is unexpectedly not just a combination of the phenotypes of the two single mutants a and b.
Fisher epistasis
PSI-MI
MI:0208
genetic interaction (sensu unexpected)
An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E
PMID:16527956
Fisher epistasis
PMID:17510664
https://doi.org/10.1017/S0080456800012163
Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
geranylgeranylation
PSI-MI
MI:0209
geranylgeranylation reaction
Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
GO:0018348
PMID:14755292
RESID:AA0104
geranylgeranylation
Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
hydroxylation
PSI-MI
MI:0210
hydroxylation reaction
Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
GO:0018126
PMID:14755292
RESID:AA0028
RESID:AA0029
RESID:AA0030
RESID:AA0146
RESID:AA0215
hydroxylation
Covalent or non covalent binding of lipid group on a protein residue.
PSI-MI
MI:0211
lipid addition
Covalent or non covalent binding of lipid group on a protein residue.
GO:0006497
PMID:14755292
Cleavage of a lipid group covalently bound to a protein residue.
lipid cleavage
PSI-MI
MI:0212
lipoprotein cleavage reaction
Cleavage of a lipid group covalently bound to a protein residue.
PMID:14755292
lipid cleavage
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
methylation
PSI-MI
MI:0213
methylation reaction
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
GO:0043414
PMID:14755292
RESID:AA0061
RESID:AA0062
RESID:AA0063
RESID:AA0064
RESID:AA0065
RESID:AA0066
RESID:AA0067
RESID:AA0068
RESID:AA0069
RESID:AA0070
RESID:AA0071
RESID:AA0072
RESID:AA0073
RESID:AA0074
RESID:AA0075
RESID:AA0076
RESID:AA0234
RESID:AA0272
methylation
Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
myristoylation
PSI-MI
MI:0214
myristoylation reaction
Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
GO:0018319
PMID:14755292
RESID:AA0059
RESID:AA0078
myristoylation
Interaction mediated by non-covalent, weak forces rearrangement.
OBSOLETE use physical interaction (MI:0218) instead.
non covalent inter
PSI-MI
MI:0215
non covalent interaction
true
Interaction mediated by non-covalent, weak forces rearrangement.
OBSOLETE use physical interaction (MI:0218) instead.
PMID:14755292
non covalent inter
Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
palmitoylation
PSI-MI
MI:0216
palmitoylation reaction
Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
GO:0018318
PMID:14755292
RESID:AA0060
RESID:AA0077
RESID:AA0079
RESID:AA0080
RESID:AA0106
palmitoylation
Reversible reaction that can affect D,C,H,S,T,Y,R residues.
phosphorylation
PSI-MI
MI:0217
phosphorylation reaction
Reversible reaction that can affect D,C,H,S,T,Y,R residues.
GO:0016310
PMID:14755292
RESID:AA0033
RESID:AA0034
RESID:AA0035
RESID:AA0036
RESID:AA0037
RESID:AA0038
RESID:AA0039
RESID:AA0222
phosphorylation
Interaction among molecules that can be direct or indirect.
OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
PSI-MI
MI:0218
physical interaction
true
Interaction among molecules that can be direct or indirect.
OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
PMID:14755292
Death phenotype observed on cells carrying combination of two independently silent mutations.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
PSI-MI
MI:0219
synthetic lethal
true
Death phenotype observed on cells carrying combination of two independently silent mutations.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
PMID:15608217
Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
ubiquitination
PSI-MI
MI:0220
ubiquitination reaction
Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
GO:0016567
PMID:11583613
RESID:AA0125
ubiquitination
Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
PSI-MI
MI:0221
expression level
Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
PMID:14755292
A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
endogenous
endogenous level
PSI-MI
MI:0222
physiological level
A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
PMID:14755292
endogenous
endogenous level
A molecule is estimated to be expressed at lower levels than in physiological condition.
under-expressed
PSI-MI
MI:0223
under expressed level
A molecule is estimated to be expressed at lower levels than in physiological condition.
PMID:14755292
under-expressed
The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
chip-chip
PSI-MI
MI:0225
chromatin immunoprecipitation array
The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
PMID:11125145
PMID:11206552
chip-chip
Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
IEC
ion exchange chrom
PSI-MI
MI:0226
ion exchange chromatography
Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
PMID:14755292
IEC
ion exchange chrom
Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
reverse phase chrom
PSI-MI
MI:0227
reverse phase chromatography
Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
PMID:14755292
reverse phase chrom
Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
cytoplasmic compl
PSI-MI
MI:0228
cytoplasmic complementation assay
true
Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
PMID:14755292
cytoplasmic compl
true
OBSOLETE remap to MI:0090 protein complementation assay.
membrane compl
PSI-MI
MI:0230
membrane bound complementation assay
true
OBSOLETE remap to MI:0090 protein complementation assay.
PMID:14755292
membrane compl
The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
mappit
PSI-MI
MI:0231
mammalian protein protein interaction trap
The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
PMID:12853652
mappit
Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
transcription compl
PSI-MI
MI:0232
transcriptional complementation assay
Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
PMID:14755292
transcription compl
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
PSI-MI
MI:0233
protein dna complex
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
PMID:14755292
Molecule labelled with 131 radio isotope of iodine atoms.
131I
I131
PSI-MI
MI:0234
131i radiolabel
Molecule labelled with 131 radio isotope of iodine atoms.
PMID:14755292
131I
I131
Molecule labelled with the radio isotope 14 of carbon atoms.
14C
C14
PSI-MI
MI:0235
14c radiolabel
Molecule labelled with the radio isotope 14 of carbon atoms.
PMID:14755292
14C
C14
Molecule labelled with the radio isotope 32 of phosphorus atoms.
32P
P32
PSI-MI
MI:0236
32p radiolabel
Molecule labelled with the radio isotope 32 of phosphorus atoms.
PMID:14755292
32P
P32
Molecule labelled with the radio isotope 33 of phosphorus atoms.
33P
P33
PSI-MI
MI:0237
33p radiolabel
Molecule labelled with the radio isotope 33 of phosphorus atoms.
PMID:14755292
33P
P33
Molecules labelled with isotope 3 of hydrogen atoms.
3H
H3
tritium
PSI-MI
MI:0238
3h radiolabel
Molecules labelled with isotope 3 of hydrogen atoms.
PMID:14755292
3H
H3
tritium
Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
PSI-MI
MI:0239
biotin tag
Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
PMID:14755292
The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
PSI-MI
MI:0240
fusion protein
The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
PMID:14755292
Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
hrp tag
PSI-MI
MI:0241
horseradish peroxidase tag
Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
PMID:14755292
hrp tag
This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
go-definition-ref
PSI-MI
MI:0242
gene ontology definition reference
This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
PMID:14755292
go-definition-ref
Reference to the master sequence from which this isoform has been derived.
isoform-parent
PSI-MI
MI:0243
isoform parent sequence reference
Reference to the master sequence from which this isoform has been derived.
PMID:14755292
isoform-parent
Collection of functional complexes within Reactome - a knowledgebase of biological processes.
http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
id-validation-regexp:
search-url:
PSI-MI
MI:0244
reactome complex
true
Collection of functional complexes within Reactome - a knowledgebase of biological processes.
http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
PMID:21067998
id-validation-regexp:
REACT_[0-9]{1,5}\.[0-9]{1,3}|[0-9]+
search-url:
http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac}
Collection of protein within the Reactome database - a knowledgebase of biological processes.
http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
id-validation-regexp:
search-url:
PSI-MI
MI:0245
reactome protein
true
Collection of protein within the Reactome database - a knowledgebase of biological processes.
http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
PMID:21067998
id-validation-regexp:
REACT_[0-9]{1,4}\.[0-9]{1,3}|[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10}
search-url:
http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=${ac}
CABRI cell lines catalogue available at.
http://www.cabri.org/
id-validation-regexp:
search-url:
PSI-MI
MI:0246
cabri
CABRI cell lines catalogue available at.
http://www.cabri.org/
PMID:14755292
id-validation-regexp:
[0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\:ACC\s[0-9]+
search-url:
http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]
New EBI Web Taxonomy.
http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
id-validation-regexp:
search-url:
PSI-MI
MI:0247
newt
true
New EBI Web Taxonomy.
http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://www.ebi.ac.uk/newt/display?search=${ac}
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
http://www.ebi.ac.uk/RESID/index.html
id-validation-regexp:
search-url:
PSI-MI
MI:0248
resid
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
http://www.ebi.ac.uk/RESID/index.html
PMID:14755292
id-validation-regexp:
AA[0-9]{4}
search-url:
http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e
A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.
http://www.kazusa.or.jp/huge/
id-validation-regexp:
search-url:
PSI-MI
MI:0249
huge
A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.
http://www.kazusa.or.jp/huge/
PMID:14755292
id-validation-regexp:
KIAA[0-9]{4}[A-Z]{0,1}
search-url:
http://www.kazusa.or.jp/huge/gfpage/${ac}
A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
PSI-MI
MI:0250
gene
A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
PMID:14755292
SO:0000704
Reference of a protein object pointing to its genomic or nucleic acid sequence.
PSI-MI
MI:0251
gene product
Reference of a protein object pointing to its genomic or nucleic acid sequence.
PMID:14755292
Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
PSI-MI
MI:0252
biological feature
Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
PMID:14755292
One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
PSI-MI
MI:0253
isotope label
One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
PMID:14755292
This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
PSI-MI
MI:0254
genetic interference
This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
PMID:14755292
This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
expression interfer
PSI-MI
MI:0255
post transcriptional interference
This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
PMID:14755292
expression interfer
RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
rnai
PSI-MI
MI:0256
rna interference
RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
PMID:12110901
PMID:12408823
rnai
This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
PSI-MI
MI:0257
antisense rna
This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
PMID:1340158
Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PSI-MI
MI:0258
inhibitor antibodies
true
Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PMID:10189716
This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
perturbagens pep
PSI-MI
MI:0259
perturbagens peptides
true
This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PMID:11731788
PMID:8606778
perturbagens pep
Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
inhibitor small mol
PSI-MI
MI:0260
inhibitor small molecules
true
Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
PMID:10542155
PMID:10780927
inhibitor small mol
A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
PSI-MI
MI:0261
obsolete suppression
true
A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
PMID:15608217
A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
PSI-MI
MI:0262
suppression mutation
true
A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
PMID:15608217
Knocked out gene is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
suppress knockout
PSI-MI
MI:0263
suppression knockout
true
Knocked out gene is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
PMID:15608217
suppress knockout
A mutation is the partial suppressor of a mutant phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
suppression partial
PSI-MI
MI:0264
suppression partial alteration
true
A mutation is the partial suppressor of a mutant phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
PMID:15608217
suppression partial
An altered expression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
suppress expression
PSI-MI
MI:0265
suppression expression alteration
true
An altered expression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
PMID:15608217
suppress expression
Overexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
suppress overexpress
PSI-MI
MI:0266
suppression overexpression
true
Overexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
PMID:15608217
suppress overexpress
Level of over/underexpression scales the 'extend' of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
PSI-MI
MI:0267
suppression scalable
true
Level of over/underexpression scales the 'extend' of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
PMID:15608217
Underexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
suppress underexpres
PSI-MI
MI:0268
suppression underexpression
true
Underexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
PMID:15608217
suppress underexpres
Two silent mutations show an altered phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
PSI-MI
MI:0269
synthetic phenotype
true
Two silent mutations show an altered phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
PMID:15608217
Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
cond syntetic lethal
PSI-MI
MI:0270
conditional synthetic lethal
true
Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
PMID:15608217
cond syntetic lethal
Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
temprtr synt lethal
PSI-MI
MI:0271
conditional synthetic lethal temperature-sensitivity
true
Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
PMID:15608217
temprtr synt lethal
Two silent mutations show altered growth effect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
synt growth effect
PSI-MI
MI:0273
synthetic growth effect
true
Two silent mutations show altered growth effect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
PMID:15608217
synt growth effect
Two silent mutations show growth defect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
synt growth defect
PSI-MI
MI:0274
synthetic growth defect
true
Two silent mutations show growth defect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
PMID:15608217
synt growth defect
Two silent mutations show growth increase when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
synt growth increase
PSI-MI
MI:0275
synthetic growth increase
true
Two silent mutations show growth increase when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
PMID:15608217
synt growth increase
Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
bn-page
PSI-MI
MI:0276
blue native page
Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
PMID:14665681
bn-page
Descriptor of type of nomenclature used to describe interactor.
CvAliasType
PSI-MI
MI:0300
alias type
Descriptor of type of nomenclature used to describe interactor.
PMID:14755292
CvAliasType
Gene name.
gene
PSI-MI
MI:0301
gene name
Gene name.
PMID:14755292
gene
Gene name synonym.
PSI-MI
MI:0302
gene name synonym
Gene name synonym.
PMID:14755292
Synonym as used in Gene Ontology.
go synonym
PSI-MI
MI:0303
gene ontology synonym
Synonym as used in Gene Ontology.
PMID:14755292
go synonym
Isoform synonym.
PSI-MI
MI:0304
isoform synonym
Isoform synonym.
PMID:14755292
A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
CDS number
ONL
ORF number
Ordered locus name
locus name
systematic gene number
PSI-MI
MI:0305
For instance HI0934, Rv3245c, At5g34500, YER456W.
ordered locus name
A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
PMID:14755292
CDS number
ONL
ORF number
Ordered locus name
locus name
systematic gene number
A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
orf name
PSI-MI
MI:0306
For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames.
open reading frame name
A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
PMID:14755292
orf name
Method by which molecule is delivered or engineered into a cell.
PSI-MI
MI:0307
delivery method
Method by which molecule is delivered or engineered into a cell.
PMID:14755292
Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
PSI-MI
MI:0308
electroporation
Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
PMID:6329708
A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.
OBSOLETE redundant term. Map to feature type : tag (MI:0507).
genetic tag insertion
PSI-MI
MI:0309
genomic tagging
true
A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.
OBSOLETE redundant term. Map to feature type : tag (MI:0507).
PMID:14755292
genetic tag insertion
Molecule introduced into a cell via an external organism, usually a virus or bacteria.
PSI-MI
MI:0310
infection
Molecule introduced into a cell via an external organism, usually a virus or bacteria.
PMID:14755292
The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
micro-injection
PSI-MI
MI:0311
microinjection
The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
PMID:3016916
micro-injection
Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
nucl transfection
PSI-MI
MI:0312
nucleic acid transfection
Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
PMID:14755292
nucl transfection
Molecular species involved in the interaction.
participant type
PSI-MI
MI:0313
interactor type
Molecular species involved in the interaction.
PMID:14755292
participant type
Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
PSI-MI
MI:0314
complex
Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
PMID:14755292
A stable set of interacting proteins that can be copurified and operate as a functional unit.
PSI-MI
MI:0315
protein complex
A stable set of interacting proteins that can be copurified and operate as a functional unit.
PMID:14755292
A macromolecular complex containing both protein and RNA molecules.
protein rna complex
ribonucleoprot compl
PSI-MI
MI:0316
ribonucleoprotein complex
A macromolecular complex containing both protein and RNA molecules.
GO:0030529
PMID:14755292
protein rna complex
ribonucleoprot compl
Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
PSI-MI
MI:0317
interaction
Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
PMID:14755292
Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
PSI-MI
MI:0318
nucleic acid
Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
PMID:14755292
SO:0000348
Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
DNA
deoxyribonucleic acid
dna
PSI-MI
MI:0319
deoxyribonucleic acid
Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
PMID:14755292
SO:0000352
DNA
deoxyribonucleic acid
dna
Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
RNA
rna
PSI-MI
MI:0320
ribonucleic acid
Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
PMID:14755292
SO:0000356
RNA
rna
Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
catalytic RNA
catalytic ribonucleic acid
crna
PSI-MI
MI:0321
catalytic rna
Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
PMID:14755292
catalytic RNA
catalytic ribonucleic acid
crna
Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
grna
guide RNA
PSI-MI
MI:0322
guide rna
Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
PMID:14755292
grna
guide RNA
A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
heterogeneous nuclear RNA
heterogeneous nuclear ribonucleic acid
hnrna
PSI-MI
MI:0323
heterogeneous nuclear rna
A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
PMID:14755292
heterogeneous nuclear RNA
heterogeneous nuclear ribonucleic acid
hnrna
Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
mRNA
mrna
PSI-MI
MI:0324
messenger rna
Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
PMID:14755292
mRNA
mrna
The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
tRNA
transfer RNA
transfer ribonucleic acid
trna
PSI-MI
MI:0325
transfer rna
The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
PMID:14755292
tRNA
transfer RNA
transfer ribonucleic acid
trna
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
PSI-MI
MI:0326
protein
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
PMID:14755292
SO:0000358
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
oligopeptide
polypeptide
PSI-MI
MI:0327
peptide
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
PMID:14755292
oligopeptide
polypeptide
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
PSI-MI
MI:0328
small molecule
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
PMID:14755292
Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
PSI-MI
MI:0329
unknown participant
Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
PMID:14755292
Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
PSI-MI
MI:0330
molecular source
Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
PMID:14755272
Molecule has been added into system from an external source or altered within the cell.
PSI-MI
MI:0331
engineered
Molecule has been added into system from an external source or altered within the cell.
PMID:14755292
Unaltered endogenous molecule in its naturally occurring state.
endogenous
PSI-MI
MI:0332
naturally occurring
Unaltered endogenous molecule in its naturally occurring state.
PMID:14755292
endogenous
Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
CvFuzzyType
endStatus
startStatus
PSI-MI
MI:0333
feature range status
Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
PMID:14755292
CvFuzzyType
endStatus
startStatus
Term describing the last amino acid of a peptide chain.
c-term
c-terminal
c-terminus
carboxy-terminus
PSI-MI
MI:0334
Displayed as 'c'.
c-terminal position
Term describing the last amino acid of a peptide chain.
PMID:14755292
c-term
c-terminal
c-terminus
carboxy-terminus
Position within the sequence clearly defined.
certain
PSI-MI
MI:0335
certain sequence position
Position within the sequence clearly defined.
PMID:14755292
certain
Partially determined sequence position known to be in a location higher than a given position.
PSI-MI
MI:0336
Displayed as '>'.
greater-than
Partially determined sequence position known to be in a location higher than a given position.
PMID:14755292
Partially determined sequence position known to be in a position lower than a given position.
PSI-MI
MI:0337
Displayed as '<'.
less-than
Partially determined sequence position known to be in a position lower than a given position.
PMID:14755292
Describes a sequence position known to be in a certain range, where the exact position is unclear.
PSI-MI
MI:0338
For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'.
range
Describes a sequence position known to be in a certain range, where the exact position is unclear.
PMID:14755292
Term describing a completely unknown or unspecified sequence position.
undetermined
PSI-MI
MI:0339
Displayed as '?'.
undetermined sequence position
Term describing a completely unknown or unspecified sequence position.
PMID:14755292
undetermined
Term describing the first amino acid of a peptide chain.
amino-terminus
n-term
n-terminal
n-terminus
PSI-MI
MI:0340
Displayed as 'n'.
n-terminal position
Term describing the first amino acid of a peptide chain.
PMID:14755292
amino-terminus
n-term
n-terminal
n-terminus
Mixture of protein forms where N-terminus has been progressively truncated.
PSI-MI
MI:0341
ragged n-terminus
Mixture of protein forms where N-terminus has been progressively truncated.
PMID:14755292
Indicates the sample context in which each interacting molecule is presented to its partner.
PSI-MI
MI:0342
sample process
Indicates the sample context in which each interacting molecule is presented to its partner.
PMID:14755292
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
PSI-MI
MI:0343
cdna library
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
PMID:6110205
Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
PSI-MI
MI:0344
cell lysate
Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
PMID:14755292
Name assigned to a molecule by the authors within a paper that may differ from the reference database.
PSI-MI
MI:0345
author assigned name
Name assigned to a molecule by the authors within a paper that may differ from the reference database.
PMID:14755292
Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
experimental prep
PSI-MI
MI:0346
experimental preparation
Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
PMID:14755292
experimental prep
Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
PSI-MI
MI:0348
fixed cell
Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
PMID:14755292
Molecule is observed within in a living cell.
PSI-MI
MI:0349
living cell
Molecule is observed within in a living cell.
PMID:14755292
Molecule has undergone one or more purification steps to isolate it from the cellular environment.
PSI-MI
MI:0350
purified
Molecule has undergone one or more purification steps to isolate it from the cellular environment.
PMID:14755292
The author states a molecule is completely pure, i.e. no other molecular species are present.
pure
PSI-MI
MI:0351
homogeneous
The author states a molecule is completely pure, i.e. no other molecular species are present.
PMID:14755292
pure
The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
PSI-MI
MI:0352
partially purified
The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
PMID:14755292
Qualifier to describe the type of information a cross-reference is pointing to.
CvXrefQualifier
refType
xref type
PSI-MI
MI:0353
cross-reference type
Qualifier to describe the type of information a cross-reference is pointing to.
PMID:14755292
CvXrefQualifier
refType
xref type
Cross reference pointing to a Gene Ontology -'cellular component' term.
search-url:
component
go component term
PSI-MI
MI:0354
cellular component
Cross reference pointing to a Gene Ontology -'cellular component' term.
PMID:14681407
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
component
go component term
Cross reference pointing to a Gene Ontology -'molecular function' term.
search-url:
function
go function term
PSI-MI
MI:0355
molecular function
Cross reference pointing to a Gene Ontology -'molecular function' term.
PMID:14681407
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
function
go function term
Reference to the corresponding object in another database. Correspondence may be complete or partial.
identity
PSI-MI
MI:0356
For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database.
identical object in an external resource
Reference to the corresponding object in another database. Correspondence may be complete or partial.
PMID:14755292
identity
Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
PSI-MI
MI:0357
method reference
Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
PMID:14755292
Used to indicate the PMID from which the experimental data is extracted.
PSI-MI
MI:0358
primary-reference
Used to indicate the PMID from which the experimental data is extracted.
PMID:14755292
Cross reference pointing to a Gene Ontology -'cellular process' term.
search-url:
go process term
process
PSI-MI
MI:0359
biological process
Cross reference pointing to a Gene Ontology -'cellular process' term.
PMID:14681407
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
go process term
process
Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
secondary-ac
PSI-MI
MI:0360
secondary accession number
Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
PMID:14755292
secondary-ac
Related object within the same database or pointing to an external database.
see-also
PSI-MI
MI:0361
additional information
Related object within the same database or pointing to an external database.
PMID:14755292
see-also
Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
modeled
modelled
PSI-MI
MI:0362
inference
Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
PMID:14755292
modeled
modelled
Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
modeled by author
modelled by author
PSI-MI
MI:0363
inferred by author
Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
PMID:14755292
modeled by author
modelled by author
Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
modeled by curator
modelled by curator
PSI-MI
MI:0364
inferred by curator
Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
PMID:14755292
modeled by curator
modelled by curator
Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
PSI-MI
MI:0365
enzyme tag
Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
PMID:10935637
Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
alk phosphatase tag
PSI-MI
MI:0366
alkaline phosphatase tag
Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
PMID:10935637
alk phosphatase tag
The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
GFP
gfp tag
green fluorescent protein
PSI-MI
MI:0367
green fluorescent protein tag
The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:7491768
GFP
gfp tag
green fluorescent protein
Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
YFP
yellow fluorescent protein
yfp tag
PSI-MI
MI:0368
yellow fluorescent protein tag
Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
PMID:10929120
YFP
yellow fluorescent protein
yfp tag
The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
gallex
PSI-MI
MI:0369
lex-a dimerization assay
The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
PMID:12446730
gallex
gallex
This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
toxcat
PSI-MI
MI:0370
tox-r dimerization assay
This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
PMID:9927659
toxcat
toxcat
Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
35S
S35
s35 radiolabelled
PSI-MI
MI:0371
35s radiolabel
Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
PMID:14755292
35S
S35
s35 radiolabelled
Cell lysates are partially fractionated to isolate a specific subcellular fraction.
subcellular prep
PSI-MI
MI:0372
subcellular preparation
Cell lysates are partially fractionated to isolate a specific subcellular fraction.
PMID:14755292
subcellular prep
Dye coupled to a molecule allowing its identification isolation and monitoring.
dye labelled
PSI-MI
MI:0373
dye label
Dye coupled to a molecule allowing its identification isolation and monitoring.
PMID:14577292
dye labelled
The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
PSI-MI
MI:0374
cyanine label
The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
PMID:14577292
The organic cyanine Cy3 emits maximally at 570 nm.
PSI-MI
MI:0375
cy3 label
The organic cyanine Cy3 emits maximally at 570 nm.
PMID:14577292
The organic cyanine Cy5 emits maximally at 670 nm.
PSI-MI
MI:0376
cy5 label
The organic cyanine Cy5 emits maximally at 670 nm.
PMID:14577292
Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
FITC labelled
fitc labelled
fluorescein isothiocyanate labbeled
PSI-MI
MI:0377
fluorescein isothiocyanate label
Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
PMID:14577292
FITC labelled
fitc labelled
fluorescein isothiocyanate labbeled
Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
rare isotope label
PSI-MI
MI:0378
rare isotope label
Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
PMID:14577292
rare isotope label
Molecules labelled with isotope 13 of carbon atoms.
13C
C13
PSI-MI
MI:0379
13c label
Molecules labelled with isotope 13 of carbon atoms.
PMID:14577292
13C
C13
Molecules labelled with isotope 15 of nytrogen atoms.
15N
N15
PSI-MI
MI:0380
15n label
Molecules labelled with isotope 15 of nytrogen atoms.
PMID:14577292
15N
N15
Molecules labelled with isotope 2 of hydrogen atoms.
2H2
D2
deuterium
PSI-MI
MI:0381
2h label
Molecules labelled with isotope 2 of hydrogen atoms.
PMID:14577292
2H2
D2
deuterium
Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
mutation increasing
PSI-MI
MI:0382
mutation increasing interaction
Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
PMID:14577292
mutation increasing
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
PSI-MI
MI:0383
biopolymer
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
PMID:14577292
All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
PSI-MI
MI:0384
alexa label
All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
PMID:10449539
Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
PSI-MI
MI:0385
alexa 350 label
Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
PMID:10449539
Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
PSI-MI
MI:0386
alexa 430 label
Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
PMID:10449539
Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
PSI-MI
MI:0387
alexa 488 label
Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
PMID:10449539
Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
PSI-MI
MI:0388
alexa 532 label
Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
PMID:10449539
Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
PSI-MI
MI:0389
alexa 546 label
Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
PMID:10449539
Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
PSI-MI
MI:0390
alexa 568 label
Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
PMID:10449539
Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
PSI-MI
MI:0391
alexa 594 label
Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
PMID:10449539
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
predetermined
PSI-MI
MI:0396
predetermined participant
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
PMID:14755292
predetermined
Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
PSI-MI
MI:0397
two hybrid array
Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
PMID:10688190
PMID:11827624
In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
two hybrid pooling
PSI-MI
MI:0398
two hybrid pooling approach
In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
PMID:11283351
PMID:20946815
two hybrid pooling
Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
2h fragment pooling
PSI-MI
MI:0399
two hybrid fragment pooling approach
Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
PMID:12634794
2h fragment pooling
Techniques which depend upon the strength of the interaction between two entities.
affinity techniques
PSI-MI
MI:0400
affinity technology
Techniques which depend upon the strength of the interaction between two entities.
PMID:14755292
affinity techniques
The application of chemical principles and methods to biological experiments to demonstrate an interaction.
PSI-MI
MI:0401
biochemical
The application of chemical principles and methods to biological experiments to demonstrate an interaction.
PMID:14755292
Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
ch-ip
PSI-MI
MI:0402
chromatin immunoprecipitation assay
Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
PMID:12054902
ch-ip
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
PSI-MI
MI:0403
colocalization
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
PMID:14755292
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
comig non denat gel
PSI-MI
MI:0404
comigration in non denaturing gel electrophoresis
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
PMID:14755292
comig non denat gel
Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
PSI-MI
MI:0405
competition binding
Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
PMID:14755292
Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
PSI-MI
MI:0406
deacetylase assay
Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
PMID:14755292
Interaction between molecules that are in direct contact with each other.
PSI-MI
MI:0407
direct interaction
Interaction between molecules that are in direct contact with each other.
PMID:14755292
Covalent bond mediated by 2 sulfur atoms.
SS-bond
disulfide bridge
PSI-MI
MI:0408
disulfide bond
Covalent bond mediated by 2 sulfur atoms.
PMID:14755292
SS-bond
disulfide bridge
Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.
OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA'
replace by:MI:0417
PSI-MI
MI:0409
dna footprinting
true
Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.
OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA'
replace by:MI:0417
PMID:14755292
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
3D-EM
electron tomog
PSI-MI
MI:0410
3D electron microscopy
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
PMID:12160704
3D-EM
electron tomog
Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
ELISA
elisa
PSI-MI
MI:0411
enzyme linked immunosorbent assay
Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
PMID:11906746
ELISA
elisa
The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
emsa supershift
PSI-MI
MI:0412
electrophoretic mobility supershift assay
The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
PMID:12169687
emsa supershift
This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
Gel retardation assay
band shift
emsa
PSI-MI
MI:0413
electrophoretic mobility shift assay
This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
PMID:12169687
Gel retardation assay
band shift
emsa
terms aiming to represent biochemical reactions referring to their resulting product modifications.
Biochemical reaction
PSI-MI
MI:0414
enzymatic reaction
terms aiming to represent biochemical reactions referring to their resulting product modifications.
PMID:14755292
Biochemical reaction
Participants are enzyme or substrate in a biochemical reaction.
PSI-MI
MI:0415
enzymatic study
Participants are enzyme or substrate in a biochemical reaction.
PMID:14755292
Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
fluorescence imaging
PSI-MI
MI:0416
fluorescence microscopy
Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
PMID:14755292
fluorescence imaging
Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
PSI-MI
MI:0417
footprinting
Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
PMID:14755292
methods supporting genetic interactions.
OBSOLETE as too unspecific use Genetic interference instead MI:0254.
PSI-MI
MI:0418
genetic
true
methods supporting genetic interactions.
OBSOLETE as too unspecific use Genetic interference instead MI:0254.
PMID:14755292
Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
GTPase
gtp hydrolisis
PSI-MI
MI:0419
gtpase assay
Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
PMID:14755292
GTPase
gtp hydrolisis
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
homogeneous time-resolved fluorescence
kinase HTRF
kinase htrf
PSI-MI
MI:0420
kinase homogeneous time resolved fluorescence
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
PMID:14987100
homogeneous time-resolved fluorescence
kinase HTRF
kinase htrf
Antibody mediated participant identification.
antibody detection
PSI-MI
MI:0421
identification by antibody
Antibody mediated participant identification.
PMID:14755292
antibody detection
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PSI-MI
MI:0422
immunostaining
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
PMID:14755292
Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
in gel kinase assay
PSI-MI
MI:0423
in-gel kinase assay
Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
PMID:14755292
in gel kinase assay
Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
PSI-MI
MI:0424
protein kinase assay
Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
PMID:14755292
Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
kinase spa
PSI-MI
MI:0425
kinase scintillation proximity assay
Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
PMID:14755292
kinase spa
Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
PSI-MI
MI:0426
light microscopy
Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
PMID:14755292
identification by mass spectrometry.
ms participant
PSI-MI
MI:0427
Identification by mass spectrometry
identification by mass spectrometry.
PMID:14755292
ms participant
Methods that provide images of molecules at various resolution depending on the technology used.
microscopy
PSI-MI
MI:0428
imaging technique
Methods that provide images of molecules at various resolution depending on the technology used.
PMID:14755292
microscopy
A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
deletion disrupting interaction
necessary binding site
required to bind
PSI-MI
MI:0429
necessary binding region
A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
PMID:14755292
required to bind
Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
nucl ac uv crosslink
PSI-MI
MI:0430
nucleic acid uv cross-linking assay
Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
PMID:14755292
nucl ac uv crosslink
Deprecated terms.
OBSOLETE term replaced by the default OBO class 'Obsolete'.
PSI-MI
MI:0431
obsolete
true
Deprecated terms.
OBSOLETE term replaced by the default OBO class 'Obsolete'.
PMID:14755292
Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
1 hybrid
one-hybrid
yeast one hybrid
yeast one-hybrid
PSI-MI
MI:0432
one hybrid
Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
PMID:10589421
1 hybrid
one-hybrid
yeast one hybrid
yeast one-hybrid
partial protein sequence identification.
partial id prot seq
PSI-MI
MI:0433
partial identification of protein sequence
partial protein sequence identification.
PMID:14755292
partial id prot seq
Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
PSI-MI
MI:0434
phosphatase assay
Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
PMID:14755292
Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
PSI-MI
MI:0435
protease assay
Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
PMID:14755292
Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
PSI-MI
MI:0436
protein footprinting
Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
PMID:14600024
PMID:14967031
PMID:14987073
Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
bridge assay
protein 3-hybrid
protein tri hybrid
trihybrid
PSI-MI
MI:0437
protein three hybrid
Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
PMID:12052864
PMID:12761205
PMID:12935900
bridge assay
protein 3-hybrid
protein tri hybrid
trihybrid
In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
Three hybrid system
rna 3-hybrid
rna tri hybrid
rna-three hybrid
PSI-MI
MI:0438
rna three hybrid
In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
PMID:12162957
PMID:8972875
Three hybrid system
rna 3-hybrid
rna tri hybrid
rna-three hybrid
A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
RSA
random-spore analysis
rsa
spore germination
PSI-MI
MI:0439
random spore analysis
A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
PMID:14755292
RSA
random-spore analysis
rsa
spore germination
Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
PSI-MI
MI:0440
saturation binding
Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
PMID:14755292
Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
SGA
sga
PSI-MI
MI:0441
synthetic genetic analysis
Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
PMID:14755292
SGA
sga
Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
sufficient binding site
sufficient to bind
PSI-MI
MI:0442
sufficient binding region
Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
PMID:14755292
sufficient to bind
Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.
OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
PSI-MI
MI:0443
ubiquitin binding
true
Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.
OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
PMID:14755292
Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
PSI-MI
MI:0444
database citation
Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
PMID:14755292
Databases acting as a source of literature information.
literature xref
publication xref
PSI-MI
MI:0445
literature database
Databases acting as a source of literature information.
PMID:14755292
literature xref
publication xref
PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central.
http://www.ncbi.nlm.nih.gov/pubmed
http://europepmc.org
id-validation-regexp:
search-url:
PSI-MI
MI:0446
pubmed
PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central.
http://www.ncbi.nlm.nih.gov/pubmed
http://europepmc.org
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://europepmc.org/abstract/MED/${ac}
A database describing a feature on a molecule.
feature xref
PSI-MI
MI:0447
feature database
A database describing a feature on a molecule.
PMID:14755292
feature xref
The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
http://www.ebi.ac.uk/GO
id-validation-regexp:
search-url:
go
PSI-MI
MI:0448
gene ontology
The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
http://www.ebi.ac.uk/GO
PMID:14755292
id-validation-regexp:
GO:[0-9]{7}
search-url:
https://www.ebi.ac.uk/QuickGO/term/${ac}
go
InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.
https://www.ebi.ac.uk/interpro/
id-validation-regexp:
search-url:
InterPro
PSI-MI
MI:0449
interpro
InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.
https://www.ebi.ac.uk/interpro/
PMID:1252001
id-validation-regexp:
IPR[0-9]{6}
search-url:
https://www.ebi.ac.uk/interpro/entry/InterPro/${ac}
InterPro
The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
id-validation-regexp:
CDD
PSI-MI
MI:0450
cdd
The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
PMID:14755292
id-validation-regexp:
[0-9]+
CDD
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
http://www.sanger.ac.uk/Software/Pfam
id-validation-regexp:
Pfam
PSI-MI
MI:0451
pfam
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
http://www.sanger.ac.uk/Software/Pfam
PMID:14755292
id-validation-regexp:
PF[0-9]{5}
Pfam
PIRSF is a classification system based on evolutionary relationship of whole proteins.
http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
id-validation-regexp:
PIRSF
PSI-MI
MI:0452
pirsf
PIRSF is a classification system based on evolutionary relationship of whole proteins.
http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
PMID:14755292
id-validation-regexp:
PIRSF[0-9]{5}
PIRSF
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
id-validation-regexp:
PRINTS
PSI-MI
MI:0453
prints
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
PMID:14755292
id-validation-regexp:
PR[0-9]{6}
PRINTS
The ProDom protein domain database consists of an automatic compilation of homologous domains.
http://protein.toulouse.inra.fr/prodom.html
id-validation-regexp:
ProDom
PSI-MI
MI:0454
prodom
The ProDom protein domain database consists of an automatic compilation of homologous domains.
http://protein.toulouse.inra.fr/prodom.html
PMID:14755292
id-validation-regexp:
PD[0-9]{6}
ProDom
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.
http://us.expasy.org/prosite/
id-validation-regexp:
Prosite
PSI-MI
MI:0455
prosite
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.
http://us.expasy.org/prosite/
PMID:14755292
id-validation-regexp:
PS[0-9]{5}
Prosite
SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
id-validation-regexp:
SCOP superfamily
PSI-MI
MI:0456
scop superfamily
SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
PMID:14755292
id-validation-regexp:
[0-9]+
SCOP superfamily
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.
http://smart.embl-heidelberg.de/
id-validation-regexp:
SMART
PSI-MI
MI:0457
smart
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.
http://smart.embl-heidelberg.de/
PMID:14755292
id-validation-regexp:
SM[0-9]{5}
SMART
TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.
http://www.tigr.org/TIGRFAMs
id-validation-regexp:
TIGRFAMs
PSI-MI
MI:0458
tigrfams
TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.
http://www.tigr.org/TIGRFAMs
PMID:14755292
id-validation-regexp:
TIGR[0-9]+
TIGRFAMs
MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.
http://www.ncbi.nlm.nih.gov/Structure
id-validation-regexp:
MMDB
PSI-MI
MI:0459
mmdb
MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.
http://www.ncbi.nlm.nih.gov/Structure
PMID:14755292
id-validation-regexp:
[0-9]+
MMDB
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
http://www.pdb.org/
id-validation-regexp:
search-url:
PDB
PSI-MI
MI:0460
rcsb pdb
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
http://www.pdb.org/
PMID:14634627
id-validation-regexp:
[0-9][a-zA-Z0-9]{3}
search-url:
http://www.pdb.org/pdb/explore/explore.do?structureId=${ac}
PDB
Databases that contain experimental or predictive molecular interaction data.
interaction xref
PSI-MI
MI:0461
interaction database
Databases that contain experimental or predictive molecular interaction data.
PMID:14755292
interaction xref
The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.
http://www.blueprint.org/bind
id-validation-regexp:
BIND
PSI-MI
MI:0462
bind
The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.
http://www.blueprint.org/bind
PMID:14755292
id-validation-regexp:
[0-9]+
BIND
The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.
http://thebiogrid.org
BioGRID
PSI-MI
MI:0463
biogrid
The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.
http://thebiogrid.org
PMID:21071413
BioGRID
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
http://mips.gsf.de/proj/yeast/CYGD.
http://mips.gsf.de/genre/proj/mpact
id-validation-regexp:
CYGD
CYGD (MIPS)
MIPS
MPact
PSI-MI
MI:0464
cygd
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
http://mips.gsf.de/proj/yeast/CYGD.
http://mips.gsf.de/genre/proj/mpact
PMID:14755292
id-validation-regexp:
[0-9]+|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]
CYGD
CYGD (MIPS)
MIPS
MPact
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.doe-mbi.ucla.edu/
id-validation-regexp:
search-url:
DIP
PSI-MI
MI:0465
dip
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.doe-mbi.ucla.edu/
PMID:14755292
id-validation-regexp:
DIP[:-]?[0-9]+[NE]
search-url:
http://identifiers.org/dip/${ac}
DIP
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.
http://ecocyc.org/
EcoCyc
PSI-MI
MI:0466
ecocyc
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.
http://ecocyc.org/
PMID:14755292
EcoCyc
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.
http://www.reactome.org/
id-validation-regexp:
search-url:
GKB
Genome Knowledge Base
Reactome
PSI-MI
MI:0467
reactome
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.
http://www.reactome.org/
PMID:21067998
id-validation-regexp:
((R-[A-Z]{3}-\d+)|(REACT_\d+))(\.\d+)?$
search-url:
http://www.reactome.org/content/detail/${ac}
GKB
Genome Knowledge Base
Reactome
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
HPRD
PSI-MI
MI:0468
hprd
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
PMID:14755292
HPRD
INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions.
http://www.ebi.ac.uk/intact
id-validation-regexp:
search-url:
IntAct
intact
PSI-MI
MI:0469
intact
INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions.
http://www.ebi.ac.uk/intact
PMID:14681455
PMID:19850723
PMID:22121220
id-validation-regexp:
EBI-[0-9]+|IA:[0-9]+
search-url:
http://www.ebi.ac.uk/intact/query/${ac}
IntAct
intact
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.
http://www.genome.ad.jp/kegg/
id-validation-regexp:
KEGG
PSI-MI
MI:0470
kegg
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.
http://www.genome.ad.jp/kegg/
PMID:14755292
id-validation-regexp:
[a-zA-Z]+:[a-zA-Z]+[0-9]+
KEGG
The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.
http://mint.bio.uniroma2.it
id-validation-regexp:
search-url:
MINT
PSI-MI
MI:0471
mint
The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.
http://mint.bio.uniroma2.it
PMID:14755292
id-validation-regexp:
MINT-[0-9]+
search-url:
https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac}
MINT
The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
http://www.ebi.ac.uk/pdbe/
id-validation-regexp:
search-url:
PQS
e-MSD
PSI-MI
MSD
MI:0472
pdbe
The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
http://www.ebi.ac.uk/pdbe/
PMID:16381867
id-validation-regexp:
[0-9][a-zA-Z0-9]{3}
search-url:
http://www.ebi.ac.uk/pdbe/entry/pdb/${ac}
PQS
Database of molecules participating in molecular interactions.
participant xref
PSI-MI
MI:0473
participant database
Database of molecules participating in molecular interactions.
PMID:14755292
participant xref
A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).
http://www.ebi.ac.uk/chebi/
id-validation-regexp:
search-url:
ChEBI
PSI-MI
MI:0474
chebi
A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).
http://www.ebi.ac.uk/chebi/
PMID:14755292
id-validation-regexp:
CHEBI:[0-9]+
search-url:
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=${ac}
ChEBI
DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.
http://www.ebi.ac.uk/embl/Contact/collaboration
id-validation-regexp:
search-url:
DDBJ
DDBJ/EMBL/GenBank
EMBL
GenBank
PSI-MI
MI:0475
ddbj/embl/genbank
DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.
http://www.ebi.ac.uk/embl/Contact/collaboration
PMID:14755292
id-validation-regexp:
[A-Z][0-9]{5}|[A-Z][0-9]{5}\.[0-9]+|[A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.[0-9]+|[A-Z]{4}[0-9]{8}|[A-Z]{4}[0-9]{8}\.[0-9]+
search-url:
http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac}
DDBJ
DDBJ/EMBL/GenBank
EMBL
GenBank
Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.
http://www.ensembl.org
id-validation-regexp:
search-url:
Ensembl
PSI-MI
MI:0476
ensembl
Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.
http://www.ensembl.org
PMID:15078858
id-validation-regexp:
ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]
search-url:
http://www.ensembl.org/Multi/Search/Results?q=${ac}
Ensembl
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
http://www.ncbi.nlm.nih.gov/LocusLink/
id-validation-regexp:
Entrez gene/locuslink
entrezgene/locuslink
PSI-MI
MI:0477
entrez gene/locuslink
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
http://www.ncbi.nlm.nih.gov/LocusLink/
PMID:14755292
id-validation-regexp:
[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+
Entrez gene/locuslink
entrezgene/locuslink
FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.
http://flybase.org
id-validation-regexp:
search-url:
FlyBase
PSI-MI
MI:0478
flybase
FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.
http://flybase.org
PMID:14755292
id-validation-regexp:
FB[a-z]{2}[0-9]{7}
search-url:
http://flybase.org/reports/${ac}
FlyBase
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
http://www.informatics.jax.org/
id-validation-regexp:
MGD/MGI
PSI-MI
MI:0479
mgd/mgi
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
http://www.informatics.jax.org/
PMID:14755292
id-validation-regexp:
MGI:[0-9]+
MGD/MGI
Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
id-validation-regexp:
search-url:
OMIM
PSI-MI
MI:0480
omim
Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
PMID:14755292
id-validation-regexp:
[0-9]+
search-url:
http://www.omim.org/entry/${ac}
OMIM
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.
http://www.ncbi.nlm.nih.gov/RefSeq/
id-validation-regexp:
Refseq
PSI-MI
MI:0481
refseq
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.
http://www.ncbi.nlm.nih.gov/RefSeq/
PMID:14755292
id-validation-regexp:
[XNZ][A-Z]_[0-9]+|[0-9]+|[XNZ][A-Z]_[0-9]+\.[0-9]+
Refseq
Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/
id-validation-regexp:
rfam
PSI-MI
MI:0482
rfam
Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/
PMID:14755292
id-validation-regexp:
RF[0-9]{5}
rfam
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.
http://rgd.mcw.edu/
id-validation-regexp:
RGD
PSI-MI
MI:0483
rgd
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.
http://rgd.mcw.edu/
PMID:14755292
id-validation-regexp:
[0-9]+
RGD
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
http://www.yeastgenome.org/
id-validation-regexp:
search-url:
SGD
Saccharomyces Genome Database
PSI-MI
MI:0484
sgd
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
http://www.yeastgenome.org/
PMID:14755292
id-validation-regexp:
S[0-9]{9}
search-url:
http://www.yeastgenome.org/locus/${ac}/overview
SGD
Saccharomyces Genome Database
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.
http://www.ebi.ac.uk/uniparc/
id-validation-regexp:
search-url:
UniParc
PSI-MI
MI:0485
uniparc
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.
http://www.ebi.ac.uk/uniparc/
PMID:14681372
id-validation-regexp:
UPI[A-F0-9]{10}
search-url:
https://www.uniprot.org/uniparc/${ac}/entry
UniParc
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
http://www.uniprot.org
id-validation-regexp:
search-url:
UniProtKB
uniprotkb
PSI-MI
MI:0486
uniprot knowledge base
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
http://www.uniprot.org
PMID:14681372
id-validation-regexp:
(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
search-url:
https://www.uniprot.org/uniprotkb/${ac}/entry
UniProtKB
uniprotkb
WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.
http://www.wormbase.org/
id-validation-regexp:
WormBase
PSI-MI
MI:0487
wormbase
WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.
http://www.wormbase.org/
PMID:14755292
id-validation-regexp:
WBGene[0-9]{8}
WormBase
PSI-MI.
id-validation-regexp:
search-url:
PSI-MI
PSI-MI
MI:0488
psi-mi
PSI-MI.
PMID:14755292
id-validation-regexp:
MI:[0-9]{4}
search-url:
http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=${ac}
PSI-MI
Database that originally provided the interaction record for exchange purposes.
PSI-MI
MI:0489
source database
Database that originally provided the interaction record for exchange purposes.
PMID:14755292
Describes the location of the experiment.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0490
experiment condition
true
Describes the location of the experiment.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Results generated by predictive bioinformatics approaches rather than experimental data.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Predictive
PSI-MI
MI:0491
in silico
true
Results generated by predictive bioinformatics approaches rather than experimental data.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Predictive
Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0492
in vitro
true
Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0493
in vivo
true
Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Literally, in place i.e. the protein is in its natural environment during the experiment.
OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PSI-MI
MI:0494
in situ
true
Literally, in place i.e. the protein is in its natural environment during the experiment.
OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
PMID:14755292
Role played by the participant within the experiment.
PSI-MI
MI:0495
experimental role
Role played by the participant within the experiment.
PMID:14755292
Molecule experimentally treated to capture its interacting partners.
PSI-MI
MI:0496
bait
Molecule experimentally treated to capture its interacting partners.
PMID:14755292
Molecule role in an experimental setting that does not have an embedded asymmetry.
PSI-MI
MI:0497
neutral component
Molecule role in an experimental setting that does not have an embedded asymmetry.
PMID:14755292
Molecule experimentally identified as being captured by a given bait.
PSI-MI
MI:0498
prey
Molecule experimentally identified as being captured by a given bait.
PMID:14755292
Role not specified or not applicable to the data.
PSI-MI
MI:0499
unspecified role
Role not specified or not applicable to the data.
PMID:14755292
Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
PSI-MI
MI:0500
biological role
Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
PMID:14755292
Molecule catalyzing a modification on its interacting partner.
PSI-MI
MI:0501
enzyme
Molecule catalyzing a modification on its interacting partner.
PMID:14755292
Molecule that is the target of its binding partner catalytic activity.
substrate
PSI-MI
MI:0502
enzyme target
Molecule that is the target of its binding partner catalytic activity.
PMID:14755292
substrate
Molecule that makes intramolecular interactions.
PSI-MI
MI:0503
self
Molecule that makes intramolecular interactions.
PMID:14755292
The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
PSI-MI
MI:0505
experimental feature
The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
PMID:14755292
A molecule is estimated to be expressed at higher levels than in physiological condition.
over-expressed
PSI-MI
MI:0506
over expressed level
A molecule is estimated to be expressed at higher levels than in physiological condition.
PMID:14755292
over-expressed
Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
PSI-MI
MI:0507
tag
Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
PMID:14755292
Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
radiolabeled acetate
PSI-MI
MI:0508
deacetylase radiometric assay
Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
PMID:14755292
radiolabeled acetate
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase.
homogeneous time-resolved fluorescence
phosphatase HTRF
phosphatase htrf
PSI-MI
MI:0509