reconstruction.ecoli.dataclasses.process.transcription_regulation

SimulationData for transcription regulation

class reconstruction.ecoli.dataclasses.process.transcription_regulation.TranscriptionRegulation(raw_data, sim_data)[source]

Bases: object

SimulationData for transcription regulation

_build_lookups(raw_data)[source]

Builds dictionaries for mapping transcription factor abbreviations to their RNA IDs, and to their active form.

get_delta_prob_matrix(dense=False, ppgpp=False)[source]

Returns the delta probability matrix mapping the promoter binding effect of each TF to each gene.

Parameters:

  • dense – If True, returns a dense matrix, otherwise csr sparse

  • ppgpp – If True, normalizes delta probabilities to be on the same scale as ppGpp normalized probabilities since delta_prob is calculated based on basal_prob which is not normalized to 1

Returns:

matrix of probabilities changes expected with a TF

binding to a promoter for each gene (n genes, m TFs)

Return type:

delta_prob

p_promoter_bound_SKd(signal, Kd, power)[source]

Computes probability of a one-component transcription factor binding promoter.

p_promoter_bound_tf(tfActive, tfInactive)[source]

Computes probability of a transcription factor binding promoter.