pypath.inputs.dorothea.tfregulons_interactions

pypath.inputs.dorothea.tfregulons_interactions(organism=9606, levels={'A', 'B', 'C', 'D'}, only_curated=False, confidence_pairwise=True)

Retrieves TF-target interactions from TF regulons.

Parameters:

• organism (int,str) – Name or NCBI Taxonomy ID of the organism. Only human is available.

• levels (set) – Confidence levels to be used.

• only_curated (bool) – Retrieve only literature curated interactions.

Details

TF regulons is a comprehensive resource of TF-target interactions combining multiple lines of evidences: literature curated databases, ChIP-Seq data, PWM based prediction using HOCOMOCO and JASPAR matrices and prediction from GTEx expression data by ARACNe. As KEGG is not longer part of the public version of DoRothEA the kegg_pathways field is always empty.

For details see saezlab/DoRothEA.