Knowledge of the perturbation design is essential for accurate gene regulatory network inference.

ABSTRACT: The gene regulatory network (GRN) of a cell executes genetic programs in response to environmental and internal cues. Two distinct classes of methods are used to infer regulatory interactions from gene expression: those that only use observed changes in gene expression, and those that use both the observed changes and the perturbation design, i.e. the targets used to cause the changes in gene expression. Considering that the GRN by definition converts input cues to changes in gene expression, it may be conjectured that the latter methods would yield more accurate inferences but this has not previously been investigated. To address this question, we evaluated a number of popular GRN inference methods that either use the perturbation design or not. For the evaluation we used targeted perturb

SUBMITTER: Secilmis D 

PROVIDER: S-EPMC9529923 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature