Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data.

ABSTRACT:

Motivation

The activity of a transcription factor (TF) in a sample of cells is the extent to which it is exerting its regulatory potential. Many methods of inferring TF activity from gene expression data have been described, but due to the lack of appropriate large-scale datasets, systematic and objective validation has not been possible until now.

Results

We systematically evaluate and optimize the approach to TF activity inference in which a gene expression matrix is factored into a condition-independent matrix of control strengths and a condition-dependent matrix of TF activity levels. We find that expression data in which the activities of individual TFs have been perturbed are both necessary and sufficient for obtaining good performance. To a considerable extent, contro

SUBMITTER: Ma CZ 

PROVIDER: S-EPMC8189679 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature