{ "cells": [ { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import numpy as np\n", "import re\n", "import sys\n", "import operator\n", "import collections\n", "import os" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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EntryEntry nameStatusProtein namesGene namesOrganismLength
0P78410BT3A2_HUMANreviewedButyrophilin subfamily 3 member A2BTN3A2 BT3.2 BTF3 BTF4Homo sapiens (Human)334
1Q8TDQ1CLM1_HUMANreviewedCMRF35-like molecule 1 (CLM-1) (CD300 antigen-...CD300LF CD300F CLM1 IGSF13 IREM1 NKIR UNQ3105/...Homo sapiens (Human)290
2Q7Z624CMKMT_HUMANreviewedCalmodulin-lysine N-methyltransferase (CLNMT) ...CAMKMT C2orf34 CLNMTHomo sapiens (Human)323
3O75208COQ9_HUMANreviewedUbiquinone biosynthesis protein COQ9, mitochon...COQ9 C16orf49 HSPC326 PSEC0129Homo sapiens (Human)318
4Q8NEV1CSK23_HUMANreviewedCasein kinase II subunit alpha 3 (CK II alpha ...CSNK2A3 CSNK2A1PHomo sapiens (Human)391
5P33681CD80_HUMANreviewedT-lymphocyte activation antigen CD80 (Activati...CD80 CD28LG CD28LG1 LAB7Homo sapiens (Human)288
6P02511CRYAB_HUMANreviewedAlpha-crystallin B chain (Alpha(B)-crystallin)...CRYAB CRYA2 HSPB5Homo sapiens (Human)175
7Q8N4T0CBPA6_HUMANreviewedCarboxypeptidase A6 (EC 3.4.17.-)CPA6 CPAHHomo sapiens (Human)437
8P20933ASPG_HUMANreviewedN(4)-(beta-N-acetylglucosaminyl)-L-asparaginas...AGAHomo sapiens (Human)346
9Q86VB7C163A_HUMANreviewedScavenger receptor cysteine-rich type 1 protei...CD163 M130Homo sapiens (Human)1156
10P53420CO4A4_HUMANreviewedCollagen alpha-4(IV) chainCOL4A4Homo sapiens (Human)1690
11A2IDD5CCD78_HUMANreviewedCoiled-coil domain-containing protein 78 (hsCC...CCDC78 C16orf25 JFP10Homo sapiens (Human)438
12Q02952AKA12_HUMANreviewedA-kinase anchor protein 12 (AKAP-12) (A-kinase...AKAP12 AKAP250Homo sapiens (Human)1782
13O15194CTDSL_HUMANreviewedCTD small phosphatase-like protein (CTDSP-like...CTDSPL C3orf8 NIF1 NIFL SCP3 YA22Homo sapiens (Human)276
14O14613BORG1_HUMANreviewedCdc42 effector protein 2 (Binder of Rho GTPase...CDC42EP2 BORG1 CEP2Homo sapiens (Human)210
15P30260CDC27_HUMANreviewedCell division cycle protein 27 homolog (Anapha...CDC27 ANAPC3 D0S1430E D17S978EHomo sapiens (Human)824
16O75175CNOT3_HUMANreviewedCCR4-NOT transcription complex subunit 3 (CCR4...CNOT3 KIAA0691 LENG2 NOT3Homo sapiens (Human)753
17Q16611BAK_HUMANreviewedBcl-2 homologous antagonist/killer (Apoptosis ...BAK1 BAK BCL2L7 CDN1Homo sapiens (Human)211
18Q07065CKAP4_HUMANreviewedCytoskeleton-associated protein 4 (63-kDa cyto...CKAP4Homo sapiens (Human)602
19Q96B67ARRD3_HUMANreviewedArrestin domain-containing protein 3 (TBP-2-li...ARRDC3 KIAA1376Homo sapiens (Human)414
20Q15327ANKR1_HUMANreviewedAnkyrin repeat domain-containing protein 1 (Ca...ANKRD1 C193 CARP HA1A2Homo sapiens (Human)319
21Q99653CHP1_HUMANreviewedCalcineurin B homologous protein 1 (Calcineuri...CHP1 CHPHomo sapiens (Human)195
22P0CG37CFC1_HUMANreviewedCryptic protein (Cryptic family protein 1)CFC1Homo sapiens (Human)223
23P17544ATF7_HUMANreviewedCyclic AMP-dependent transcription factor ATF-...ATF7 ATFAHomo sapiens (Human)494
24Q8N5B7CERS5_HUMANreviewedCeramide synthase 5 (CerS5) (EC 2.3.1.-) (LAG1...CERS5 LASS5Homo sapiens (Human)392
25Q6ZMG9CERS6_HUMANreviewedCeramide synthase 6 (CerS6) (EC 2.3.1.-) (LAG1...CERS6 LASS6Homo sapiens (Human)384
26A0A1B0GW15A0A1B0GW15_HUMANunreviewedUncharacterized proteinNaNHomo sapiens (Human)77
27A0A0A0MRX4A0A0A0MRX4_HUMANunreviewedRal guanine nucleotide dissociation stimulator...RGL3Homo sapiens (Human)710
28F5H052F5H052_HUMANunreviewedArmadillo repeat-containing protein 6 (Fragment)ARMC6Homo sapiens (Human)103
29B1AMT0B1AMT0_HUMANunreviewedCohesin subunit SA-2 (Fragment)STAG2Homo sapiens (Human)115
........................
74004O14775GNB5_HUMANreviewedGuanine nucleotide-binding protein subunit bet...GNB5Homo sapiens (Human)395
74005O43716GATC_HUMANreviewedGlutamyl-tRNA(Gln) amidotransferase subunit C,...GATC 15E1.2Homo sapiens (Human)136
74006P03372ESR1_HUMANreviewedEstrogen receptor (ER) (ER-alpha) (Estradiol r...ESR1 ESR NR3A1Homo sapiens (Human)595
74007Q6NT32EST5A_HUMANreviewedCarboxylesterase 5A (EC 3.1.1.1) (Carboxyleste...CES5A CES7Homo sapiens (Human)575
74008P30793GCH1_HUMANreviewedGTP cyclohydrolase 1 (EC 3.5.4.16) (GTP cycloh...GCH1 DYT5 GCHHomo sapiens (Human)250
74009Q9HAH7FBRS_HUMANreviewedProbable fibrosin-1FBRS FBS FBS1Homo sapiens (Human)460
74010O00461GOLI4_HUMANreviewedGolgi integral membrane protein 4 (Golgi integ...GOLIM4 GIMPC GOLPH4 GPP130Homo sapiens (Human)696
74011Q9UI32GLSL_HUMANreviewedGlutaminase liver isoform, mitochondrial (GLS)...GLS2 GAHomo sapiens (Human)602
74012Q9UBI6GBG12_HUMANreviewedGuanine nucleotide-binding protein G(I)/G(S)/G...GNG12Homo sapiens (Human)72
74013P63215GBG3_HUMANreviewedGuanine nucleotide-binding protein G(I)/G(S)/G...GNG3 GNGT3Homo sapiens (Human)75
74014Q8WUU5GATD1_HUMANreviewedGATA zinc finger domain-containing protein 1 (...GATAD1 ODAGHomo sapiens (Human)269
74015Q8NBI3DRAXI_HUMANreviewedDraxin (Dorsal inhibitory axon guidance protei...DRAXIN C1orf187 PSEC0258 UNQ3119/PRO10268Homo sapiens (Human)349
74016Q8IUC8GLT13_HUMANreviewedPolypeptide N-acetylgalactosaminyltransferase ...GALNT13 KIAA1918Homo sapiens (Human)556
74017Q7Z2K6ERMP1_HUMANreviewedEndoplasmic reticulum metallopeptidase 1 (EC 3...ERMP1 FXNA KIAA1815Homo sapiens (Human)904
74018Q9UM22EPDR1_HUMANreviewedMammalian ependymin-related protein 1 (MERP-1)...EPDR1 MERP1 UCC1Homo sapiens (Human)224
74019P05160F13B_HUMANreviewedCoagulation factor XIII B chain (Fibrin-stabil...F13BHomo sapiens (Human)661
74020P37059DHB2_HUMANreviewedEstradiol 17-beta-dehydrogenase 2 (EC 1.1.1.62...HSD17B2 EDH17B2 SDR9C2Homo sapiens (Human)387
74021A8K855EFCB7_HUMANreviewedEF-hand calcium-binding domain-containing prot...EFCAB7 KIAA1799Homo sapiens (Human)629
74022Q16099GRIK4_HUMANreviewedGlutamate receptor ionotropic, kainate 4 (GluK...GRIK4 GRIKHomo sapiens (Human)956
74023P0DPD8EFCE2_HUMANreviewedEEF1AKMT4-ECE2 readthrough transcript protein ...EEF1AKMT4-ECE2Homo sapiens (Human)883
74024P56937DHB7_HUMANreviewed3-keto-steroid reductase (EC 1.1.1.270) (17-be...HSD17B7 SDR37C1 UNQ2563/PRO6243Homo sapiens (Human)341
74025Q9NYF3FA53C_HUMANreviewedProtein FAM53CFAM53C C5orf6Homo sapiens (Human)392
74026Q6UY11DLK2_HUMANreviewedProtein delta homolog 2 (DLK-2) (Epidermal gro...DLK2 EGFL9 UNQ2903/PRO28633Homo sapiens (Human)383
74027Q99504EYA3_HUMANreviewedEyes absent homolog 3 (EC 3.1.3.48)EYA3Homo sapiens (Human)573
74028Q01459DIAC_HUMANreviewedDi-N-acetylchitobiase (EC 3.2.1.-)CTBS CTBHomo sapiens (Human)385
74029O60610DIAP1_HUMANreviewedProtein diaphanous homolog 1 (Diaphanous-relat...DIAPH1 DIAP1Homo sapiens (Human)1272
74030O60269GRIN2_HUMANreviewedG protein-regulated inducer of neurite outgrow...GPRIN2 KIAA0514Homo sapiens (Human)458
74031Q6P3S1DEN1B_HUMANreviewedDENN domain-containing protein 1B (Connecdenn ...DENND1B C1orf218 FAM31BHomo sapiens (Human)775
74032P09958FURIN_HUMANreviewedFurin (EC 3.4.21.75) (Dibasic-processing enzym...FURIN FUR PACE PCSK3Homo sapiens (Human)794
74033Q8IUX8EGFL6_HUMANreviewedEpidermal growth factor-like protein 6 (EGF-li...EGFL6 MAEG PP648 UNQ281/PRO320Homo sapiens (Human)553
\n", "

74034 rows × 7 columns

\n", "
" ], "text/plain": [ " Entry Entry name Status \\\n", "0 P78410 BT3A2_HUMAN reviewed \n", "1 Q8TDQ1 CLM1_HUMAN reviewed \n", "2 Q7Z624 CMKMT_HUMAN reviewed \n", "3 O75208 COQ9_HUMAN reviewed \n", "4 Q8NEV1 CSK23_HUMAN reviewed \n", "... ... ... ... \n", "74029 O60610 DIAP1_HUMAN reviewed \n", "74030 O60269 GRIN2_HUMAN reviewed \n", "74031 Q6P3S1 DEN1B_HUMAN reviewed \n", "74032 P09958 FURIN_HUMAN reviewed \n", "74033 Q8IUX8 EGFL6_HUMAN reviewed \n", "\n", " Protein names \\\n", "0 Butyrophilin subfamily 3 member A2 \n", "1 CMRF35-like molecule 1 (CLM-1) (CD300 antigen-... \n", "2 Calmodulin-lysine N-methyltransferase (CLNMT) ... \n", "3 Ubiquinone biosynthesis protein COQ9, mitochon... \n", "4 Casein kinase II subunit alpha 3 (CK II alpha ... \n", "... ... \n", "74029 Protein diaphanous homolog 1 (Diaphanous-relat... \n", "74030 G protein-regulated inducer of neurite outgrow... \n", "74031 DENN domain-containing protein 1B (Connecdenn ... \n", "74032 Furin (EC 3.4.21.75) (Dibasic-processing enzym... \n", "74033 Epidermal growth factor-like protein 6 (EGF-li... \n", "\n", " Gene names \\\n", "0 BTN3A2 BT3.2 BTF3 BTF4 \n", "1 CD300LF CD300F CLM1 IGSF13 IREM1 NKIR UNQ3105/... \n", "2 CAMKMT C2orf34 CLNMT \n", "3 COQ9 C16orf49 HSPC326 PSEC0129 \n", "4 CSNK2A3 CSNK2A1P \n", "... ... \n", "74029 DIAPH1 DIAP1 \n", "74030 GPRIN2 KIAA0514 \n", "74031 DENND1B C1orf218 FAM31B \n", "74032 FURIN FUR PACE PCSK3 \n", "74033 EGFL6 MAEG PP648 UNQ281/PRO320 \n", "\n", " Organism Length \n", "0 Homo sapiens (Human) 334 \n", "1 Homo sapiens (Human) 290 \n", "2 Homo sapiens (Human) 323 \n", "3 Homo sapiens (Human) 318 \n", "4 Homo sapiens (Human) 391 \n", "... ... ... \n", "74029 Homo sapiens (Human) 1272 \n", "74030 Homo sapiens (Human) 458 \n", "74031 Homo sapiens (Human) 775 \n", "74032 Homo sapiens (Human) 794 \n", "74033 Homo sapiens (Human) 553 \n", "\n", "[74034 rows x 7 columns]" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "bioplex_interactions = pd.read_csv('Uniprot_Proteome.tsv', sep='\\t')\n", "\n", "bioplex_interactions" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['BTN3A2',\n", " 'BT3.2',\n", " 'BTF3',\n", " 'BTF4',\n", " 'CD300LF',\n", " 'CD300F',\n", " 'CLM1',\n", " 'IGSF13',\n", " 'IREM1',\n", " 'NKIR',\n", " 'UNQ3105/PRO10111',\n", " 'CAMKMT',\n", " 'C2orf34',\n", " 'CLNMT',\n", " 'COQ9',\n", " 'C16orf49',\n", " 'HSPC326',\n", " 'PSEC0129',\n", " 'CSNK2A3',\n", " 'CSNK2A1P',\n", " 'CD80',\n", " 'CD28LG',\n", " 'CD28LG1',\n", " 'LAB7',\n", " 'CRYAB',\n", " 'CRYA2',\n", " 'HSPB5',\n", " 'CPA6',\n", " 'CPAH',\n", " 'AGA',\n", " 'CD163',\n", " 'M130',\n", " 'COL4A4',\n", " 'CCDC78',\n", " 'C16orf25',\n", " 'JFP10',\n", " 'AKAP12',\n", " 'AKAP250',\n", " 'CTDSPL',\n", " 'C3orf8',\n", " 'NIF1',\n", " 'NIFL',\n", " 'SCP3',\n", " 'YA22',\n", " 'CDC42EP2',\n", " 'BORG1',\n", " 'CEP2',\n", " 'CDC27',\n", " 'ANAPC3',\n", " 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'DEPDC4',\n", " 'PIGT',\n", " 'SMYD4',\n", " 'SLC37A3',\n", " 'MAPK10',\n", " 'ARPP21',\n", " 'STIM2',\n", " 'SLC25A29',\n", " 'SH2D4A',\n", " 'FBXL5',\n", " 'APOC1',\n", " 'C1orf167',\n", " 'ZNF10',\n", " 'LGR4',\n", " 'RCN2',\n", " 'DHX36',\n", " 'DIABLO',\n", " 'LRRK2',\n", " 'CS',\n", " 'ZNF816',\n", " 'ADGRG1',\n", " 'KCNN3',\n", " 'DDX3X',\n", " 'RHBDF2',\n", " 'NAA38',\n", " 'PSMC3',\n", " 'MCIDAS',\n", " 'PRAMEF9',\n", " 'EXT2',\n", " 'RPS6KA5',\n", " 'PIGQ',\n", " 'MBP',\n", " 'TXNDC9',\n", " 'SREBF2',\n", " 'YIF1B',\n", " 'TRAJ33',\n", " 'SLC46A2',\n", " 'TMEM248',\n", " 'ANKRD12',\n", " 'PEG3',\n", " 'HBP1',\n", " 'RNF123',\n", " 'PHACTR4',\n", " 'USP17L19',\n", " 'RAB5A',\n", " 'SHPRH',\n", " 'HLA-DMA',\n", " 'CAMK2D',\n", " 'USE1',\n", " 'RFX2',\n", " 'RFX4',\n", " 'ZNF683',\n", " 'MBD6',\n", " 'NDRG4',\n", " 'CNTRL',\n", " 'CASP7',\n", " 'KIF1B',\n", " 'DIRAS2',\n", " 'ADD1',\n", " 'C6orf52',\n", " 'MOK',\n", " 'MEIS2',\n", " 'DNMBP',\n", " 'LSM7',\n", " 'CEP126',\n", " 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'AMT',\n", " 'FRMPD2',\n", " 'C3orf67',\n", " 'CCAR1',\n", " 'SULF1',\n", " 'PLK1',\n", " 'FARSA',\n", " 'MED15',\n", " 'IGKV1OR2-108',\n", " 'TBCE',\n", " 'FAM107B',\n", " 'LARP1B',\n", " 'TENM3',\n", " 'DLG1',\n", " 'NUDCD2',\n", " 'MYO5A',\n", " 'ASF1B',\n", " 'CA11',\n", " 'CRYGN',\n", " 'WNK2',\n", " 'COPS6',\n", " 'PUM2',\n", " 'PDE6D',\n", " 'ARHGAP4',\n", " 'DAB2',\n", " 'FKBP7',\n", " 'CASC3',\n", " 'NCK1',\n", " 'MLXIP',\n", " 'ALDH1L1',\n", " 'GALE',\n", " 'GLB1',\n", " 'PYM1',\n", " 'RNF214',\n", " 'RBM47',\n", " 'PUF60',\n", " 'AKAP13',\n", " 'KPNB1',\n", " 'TRAJ46',\n", " 'CCDC178',\n", " 'HAUS4',\n", " 'NDC80',\n", " 'SLC35B1',\n", " 'TMPRSS5',\n", " 'SERPING1',\n", " 'SAP30BP',\n", " 'MPDU1',\n", " 'GM2A',\n", " 'SLC20A1',\n", " 'NUCB2',\n", " 'NVL',\n", " 'ARHGEF10L',\n", " 'GC',\n", " 'CEP192',\n", " 'RHOH',\n", " 'N4BP2L1',\n", " 'PALM3',\n", " 'SNRNP70',\n", " 'NMNAT3',\n", " 'AMDHD1',\n", " 'PCYT1A',\n", " 'ZNF793',\n", " 'C4orf19',\n", " 'TACC1',\n", " 'VWDE',\n", " 'HLA-DPB1',\n", " 'ARPC1A',\n", " 'GALNS',\n", " 'TXNDC12',\n", " 'GNLY',\n", " 'PRDM16',\n", " 'CFLAR',\n", " 'ACTR6',\n", " 'RAB30',\n", " 'CPNE3',\n", " 'MUC1',\n", " 'FBXO22',\n", " 'CP',\n", " 'BET1L',\n", " 'RSRC1',\n", " 'ZNF175',\n", " 'SPECC1',\n", " 'FARS2',\n", " 'TTC32',\n", " 'COX7A2',\n", " 'RNPEPL1',\n", " 'RABEPK',\n", " 'BCL7C',\n", " 'UMODL1',\n", " 'PTPA',\n", " 'CYFIP2',\n", " 'BBX',\n", " 'GNAS',\n", " 'USP10',\n", " 'DCN',\n", " 'HSPA9',\n", " 'ZFAND2B',\n", " 'POLR3E',\n", " 'CTDP1',\n", " 'AP1S3',\n", " 'HLA-C',\n", " 'FAP',\n", " 'CMSS1',\n", " 'CARM1',\n", " 'RINL',\n", " 'FXR2',\n", " 'ST7',\n", " 'JADE3',\n", " 'EXOC7',\n", " 'HMGXB4',\n", " 'VPS33B',\n", " 'CPNE1',\n", " 'RAP1B',\n", " 'MACF1',\n", " 'CNPY2',\n", " 'CCDC97',\n", " 'IL16',\n", " 'CCDC106',\n", " ...]" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "prot_list = []\n", "for ind, row in bioplex_interactions.iterrows():\n", " prots = str(row['Gene names'])\n", " #print(prots)\n", " prot_arr = prots.split(' ')\n", " #print(prot_arr)\n", " for prot in prot_arr:\n", " if prot not in prot_list:\n", " prot_list.append(prot)\n", " \n", "prot_list" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "45637\n" ] } ], "source": [ "print(len(prot_list))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.8" } }, "nbformat": 4, "nbformat_minor": 2 }