Predict expression modulation targets
=====================================
Cameo provides algorithms to search for genes or reactions that can be
over- or down-regulated in order to achieve a given biological
objective.
.. code:: ipython3
from cameo import models
from cameo.visualization.plotting.with_plotly import PlotlyPlotter
Load the E. coli core model.
.. code:: ipython3
model = models.bigg.e_coli_core
plotter = PlotlyPlotter()
Flux Scanning based on Enforced Objective Flux
----------------------------------------------
.. code:: ipython3
from cameo.strain_design.deterministic.flux_variability_based import FSEOF
.. code:: ipython3
fseof = FSEOF(model)
.. code:: ipython3
fseof.run(target=model.reactions.EX_succ_e)
.. raw:: html
Model: e_coli_core
Enforced objective: EX_succ_e
Primary objective: Maximize
1.0*BIOMASS_Ecoli_core_w_GAM - 1.0*BIOMASS_Ecoli_core_w_GAM_reverse_712e5
Reaction fluxes
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | |
---|---|---|---|---|---|---|---|---|---|---|
PFK | 7.756941 | 8.036499 | 8.242515 | 8.361048 | 8.479582 | 8.598115 | 8.747793 | 9.393102 | 9.830787 | 9.910940 |
PGI | 5.485630 | 6.110399 | 6.513173 | 6.651876 | 6.790579 | 6.929282 | 7.161108 | 8.874882 | 9.965126 | 9.981645 |
PGK | -16.431132 | -16.838737 | -17.173618 | -17.421989 | -17.670359 | -17.918730 | -18.198431 | -18.976723 | -19.547784 | -19.761991 |
PGM | -15.238892 | -15.761645 | -16.212407 | -16.577535 | -16.942662 | -17.307790 | -17.704415 | -18.602292 | -19.293292 | -19.628048 |
PPC | 3.758320 | 5.012330 | 5.878875 | 6.284516 | 6.690157 | 7.095799 | 7.532996 | 8.472367 | 9.615323 | 11.108854 |
PPS | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.410338 | 1.527283 |
ADK1 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.410338 | 1.527283 |
ENO | 15.238892 | 15.761645 | 16.212407 | 16.577535 | 16.942662 | 17.307790 | 17.704415 | 18.602292 | 19.293292 | 19.628048 |
SUCCt3 | 1.474575 | 2.949150 | 4.423725 | 5.898300 | 7.372875 | 8.847450 | 10.322025 | 11.796600 | 13.271175 | 14.745750 |
THD2 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.119674 | 2.143848 | 2.916807 | 1.535161 |
TPI | 7.756941 | 8.036499 | 8.242515 | 8.361048 | 8.479582 | 8.598115 | 8.747793 | 9.393102 | 9.830787 | 9.910940 |
FBA | 7.756941 | 8.036499 | 8.242515 | 8.361048 | 8.479582 | 8.598115 | 8.747793 | 9.393102 | 9.830787 | 9.910940 |
FRD7 | 0.000000 | 0.000000 | 0.000000 | 1.453235 | 3.175302 | 4.897369 | 6.586703 | 7.755141 | 9.127842 | 10.852285 |
GAPD | 16.431132 | 16.838737 | 17.173618 | 17.421989 | 17.670359 | 17.918730 | 18.198431 | 18.976723 | 19.547784 | 19.761991 |
ICL | 0.000000 | 0.000000 | 0.386057 | 1.231342 | 2.076627 | 2.921912 | 3.735322 | 4.041459 | 4.143333 | 3.893465 |
MALS | 0.000000 | 0.000000 | 0.386057 | 1.231342 | 2.076627 | 2.921912 | 3.735322 | 4.041459 | 4.143333 | 3.893465 |
PDH | 8.809270 | 8.336008 | 8.179868 | 8.400957 | 8.622045 | 8.843134 | 9.064539 | 9.290984 | 9.107760 | 8.219084 |
EX_succ_e | 1.474575 | 2.949150 | 4.423725 | 5.898300 | 7.372875 | 8.847450 | 10.322025 | 11.796600 | 13.271175 | 14.745750 |
lower_bound | upper_bound | gaps | normalized_gaps | biomass | production | KO | flux_reversal | suddenly_essential | free_flux | reaction | excluded | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
reaction | ||||||||||||
ACALD | 0.000000 | 0.000000 | -8.279455 | NaN | 0.000000 | 13.905778 | True | False | False | False | ACALD | False |
ACALDt | 0.000000 | 0.000000 | 0.000000 | NaN | 0.000000 | 13.905778 | True | False | False | False | ACALDt | False |
ACKr | -5.664889 | -5.664889 | -2.838696 | NaN | 0.000000 | 13.905778 | False | False | False | False | ACKr | False |
ACONTa | 0.429333 | 0.429333 | 0.200970 | NaN | 0.000000 | 13.905778 | False | False | False | False | ACONTa | False |
ACONTb | 0.429333 | 0.429333 | 0.200970 | NaN | 0.000000 | 13.905778 | False | False | False | False | ACONTb | False |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
TALA | -0.033659 | -0.033659 | -0.004207 | 0.000000 | 0.188145 | 2.123333 | False | False | False | False | TALA | False |
THD2 | 3.225950 | 3.225950 | -0.403244 | 0.000000 | 0.188145 | 2.123333 | False | False | False | False | THD2 | False |
TKT1 | -0.033659 | -0.033659 | -0.004207 | 0.000000 | 0.188145 | 2.123333 | False | False | False | False | TKT1 | False |
TKT2 | -0.101579 | -0.101579 | -0.012697 | 0.000000 | 0.188145 | 2.123333 | False | False | False | False | TKT2 | False |
TPI | 9.812852 | 9.812852 | 0.023393 | 5.905616 | 0.188145 | 2.123333 | False | False | False | False | TPI | False |
684 rows × 12 columns