Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs.

ABSTRACT: Understanding the role of transcription and transcription factors in cellular identity and disease, such as cancer and autoimmunity, is essential. However, comprehensive data resources for cell line-specific transcription factor-to-target gene annotations are currently limited. To address this, we developed a straightforward method to define regulons that capture the cell-specific aspects of TF binding and transcript expression levels. By integrating cellular transcriptome and transcription factor binding data, we generated regulons for four common cell lines comprising both proximal and distal cell line-specific regulatory events. Through systematic benchmarking involving transcription factor knockout experiments, we demonstrated performance on par with state-of-the-art methods, with our

SUBMITTER: Minaeva M 

PROVIDER: S-EPMC10802353 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature