Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases.

ABSTRACT: Gene expression is controlled by pathways of regulatory factors often involving the activity of protein kinases on transcription factor proteins. Despite this well established mechanism, the number of well described pathways that include the regulatory role of protein kinases on transcription factors is surprisingly scarce in eukaryotes. To address this, PhosTF was developed to infer functional regulatory interactions and pathways in both simulated and real biological networks, based on linear cyclic causal models with latent variables. GeneNetWeaverPhos, an extension of GeneNetWeaver, was developed to allow the simulation of perturbations in known networks that included the activity of protein kinases and phosphatases on gene regulation. Over 2000 genome-wide gene expression profiles, whe

SUBMITTER: Madsen CD 

PROVIDER: S-EPMC9255832 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature