3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin

STAR Protoc. 2022 May 11;3(2):101382. doi: 10.1016/j.xpro.2022.101382. eCollection 2022 Jun 17.

Abstract

Precise identification of context-specific transcriptional regulators (TRs) cooperation facilitates the understanding of complex gene regulation. However, previous methods are highly reliant on the availability of ChIPped TRs. Here, we provide a protocol for running 3DCoop, a pipeline for computational inference of cell type-specific TR cooperation in 3D chromatin by integrating TR motifs, open chromatin profiles, gene expression, and chromatin loops. 3DCoop provides a feasible solution to study the potential interplay among TRs across multiple human or mouse tissue/cell types. For complete details on the use and execution of this protocol, please refer to Yi et al. (2021).

Keywords: Bioinformatics; Gene Expression; Genetics; Genomics; Systems biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin* / genetics
  • Gene Expression Regulation
  • Humans
  • Mice
  • Transcription Factors* / genetics

Substances

  • Chromatin
  • Transcription Factors