{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Predict expression modulation targets\n",
"\n",
"Cameo provides algorithms to search for genes or reactions that can be over- or down-regulated in order to achieve a given biological objective."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from cameo import models\n",
"from cameo.visualization.plotting.with_plotly import PlotlyPlotter"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Load the E. coli core model."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"model = models.bigg.e_coli_core\n",
"plotter = PlotlyPlotter()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Flux Scanning based on Enforced Objective Flux"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"from cameo.strain_design.deterministic.flux_variability_based import FSEOF"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"fseof = FSEOF(model)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"Model: e_coli_core\n",
"Enforced objective: EX_succ_e\n",
"Primary objective: Maximize\n",
"1.0*BIOMASS_Ecoli_core_w_GAM - 1.0*BIOMASS_Ecoli_core_w_GAM_reverse_712e5\n",
"
\n",
"Reaction fluxes
\n",
"
\n", " | 1 | \n", "2 | \n", "3 | \n", "4 | \n", "5 | \n", "6 | \n", "7 | \n", "8 | \n", "9 | \n", "10 | \n", "
---|---|---|---|---|---|---|---|---|---|---|
PFK | \n", "7.756941 | \n", "8.036499 | \n", "8.242515 | \n", "8.361048 | \n", "8.479582 | \n", "8.598115 | \n", "8.747793 | \n", "9.393102 | \n", "9.830787 | \n", "9.910940 | \n", "
PGI | \n", "5.485630 | \n", "6.110399 | \n", "6.513173 | \n", "6.651876 | \n", "6.790579 | \n", "6.929282 | \n", "7.161108 | \n", "8.874882 | \n", "9.965126 | \n", "9.981645 | \n", "
PGK | \n", "-16.431132 | \n", "-16.838737 | \n", "-17.173618 | \n", "-17.421989 | \n", "-17.670359 | \n", "-17.918730 | \n", "-18.198431 | \n", "-18.976723 | \n", "-19.547784 | \n", "-19.761991 | \n", "
PGM | \n", "-15.238892 | \n", "-15.761645 | \n", "-16.212407 | \n", "-16.577535 | \n", "-16.942662 | \n", "-17.307790 | \n", "-17.704415 | \n", "-18.602292 | \n", "-19.293292 | \n", "-19.628048 | \n", "
PPC | \n", "3.758320 | \n", "5.012330 | \n", "5.878875 | \n", "6.284516 | \n", "6.690157 | \n", "7.095799 | \n", "7.532996 | \n", "8.472367 | \n", "9.615323 | \n", "11.108854 | \n", "
PPS | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.410338 | \n", "1.527283 | \n", "
ADK1 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.410338 | \n", "1.527283 | \n", "
ENO | \n", "15.238892 | \n", "15.761645 | \n", "16.212407 | \n", "16.577535 | \n", "16.942662 | \n", "17.307790 | \n", "17.704415 | \n", "18.602292 | \n", "19.293292 | \n", "19.628048 | \n", "
SUCCt3 | \n", "1.474575 | \n", "2.949150 | \n", "4.423725 | \n", "5.898300 | \n", "7.372875 | \n", "8.847450 | \n", "10.322025 | \n", "11.796600 | \n", "13.271175 | \n", "14.745750 | \n", "
THD2 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.119674 | \n", "2.143848 | \n", "2.916807 | \n", "1.535161 | \n", "
TPI | \n", "7.756941 | \n", "8.036499 | \n", "8.242515 | \n", "8.361048 | \n", "8.479582 | \n", "8.598115 | \n", "8.747793 | \n", "9.393102 | \n", "9.830787 | \n", "9.910940 | \n", "
FBA | \n", "7.756941 | \n", "8.036499 | \n", "8.242515 | \n", "8.361048 | \n", "8.479582 | \n", "8.598115 | \n", "8.747793 | \n", "9.393102 | \n", "9.830787 | \n", "9.910940 | \n", "
FRD7 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "1.453235 | \n", "3.175302 | \n", "4.897369 | \n", "6.586703 | \n", "7.755141 | \n", "9.127842 | \n", "10.852285 | \n", "
GAPD | \n", "16.431132 | \n", "16.838737 | \n", "17.173618 | \n", "17.421989 | \n", "17.670359 | \n", "17.918730 | \n", "18.198431 | \n", "18.976723 | \n", "19.547784 | \n", "19.761991 | \n", "
ICL | \n", "0.000000 | \n", "0.000000 | \n", "0.386057 | \n", "1.231342 | \n", "2.076627 | \n", "2.921912 | \n", "3.735322 | \n", "4.041459 | \n", "4.143333 | \n", "3.893465 | \n", "
MALS | \n", "0.000000 | \n", "0.000000 | \n", "0.386057 | \n", "1.231342 | \n", "2.076627 | \n", "2.921912 | \n", "3.735322 | \n", "4.041459 | \n", "4.143333 | \n", "3.893465 | \n", "
PDH | \n", "8.809270 | \n", "8.336008 | \n", "8.179868 | \n", "8.400957 | \n", "8.622045 | \n", "8.843134 | \n", "9.064539 | \n", "9.290984 | \n", "9.107760 | \n", "8.219084 | \n", "
EX_succ_e | \n", "1.474575 | \n", "2.949150 | \n", "4.423725 | \n", "5.898300 | \n", "7.372875 | \n", "8.847450 | \n", "10.322025 | \n", "11.796600 | \n", "13.271175 | \n", "14.745750 | \n", "
\n", " | lower_bound | \n", "upper_bound | \n", "gaps | \n", "normalized_gaps | \n", "biomass | \n", "production | \n", "KO | \n", "flux_reversal | \n", "suddenly_essential | \n", "free_flux | \n", "reaction | \n", "excluded | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
reaction | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
ACALD | \n", "0.000000 | \n", "0.000000 | \n", "-8.279455 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "True | \n", "False | \n", "False | \n", "False | \n", "ACALD | \n", "False | \n", "
ACALDt | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "True | \n", "False | \n", "False | \n", "False | \n", "ACALDt | \n", "False | \n", "
ACKr | \n", "-5.664889 | \n", "-5.664889 | \n", "-2.838696 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACKr | \n", "False | \n", "
ACONTa | \n", "0.429333 | \n", "0.429333 | \n", "0.200970 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACONTa | \n", "False | \n", "
ACONTb | \n", "0.429333 | \n", "0.429333 | \n", "0.200970 | \n", "NaN | \n", "0.000000 | \n", "13.905778 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ACONTb | \n", "False | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
TALA | \n", "-0.033659 | \n", "-0.033659 | \n", "-0.004207 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TALA | \n", "False | \n", "
THD2 | \n", "3.225950 | \n", "3.225950 | \n", "-0.403244 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "THD2 | \n", "False | \n", "
TKT1 | \n", "-0.033659 | \n", "-0.033659 | \n", "-0.004207 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TKT1 | \n", "False | \n", "
TKT2 | \n", "-0.101579 | \n", "-0.101579 | \n", "-0.012697 | \n", "0.000000 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TKT2 | \n", "False | \n", "
TPI | \n", "9.812852 | \n", "9.812852 | \n", "0.023393 | \n", "5.905616 | \n", "0.188145 | \n", "2.123333 | \n", "False | \n", "False | \n", "False | \n", "False | \n", "TPI | \n", "False | \n", "
684 rows × 12 columns
\n", "