Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP.

ABSTRACT: Deciphering the underlying gene regulatory networks (GRNs) that govern early human embryogenesis is critical for understanding developmental mechanisms yet remains challenging due to limited sample availability and the inherent complexity of the biological processes involved. To address this, we developed InPheRNo-ChIP, a computational framework that integrates multimodal data, including RNA-seq, transcription factor (TF)-specific ChIP-seq, and phenotypic labels, to reconstruct phenotype-relevant GRNs associated with endoderm development. The core of this method is a probabilistic graphical model that models the simultaneous effect of TFs on their putative target genes to influence a particular phenotypic outcome. Unlike the majority of existing GRN inference methods that are agnostic to t

SUBMITTER: Su C 

PROVIDER: S-EPMC11558691 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature