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

Xianfu Yi; Menghan Luo; Xiangling Feng; Yao Zhou; Jianhua Wang; Mulin Jun Li

doi:10.1016/j.xpro.2022.101382

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.

Authors

Xianfu Yi^{1

2}, Menghan Luo¹, Xiangling Feng¹, Yao Zhou¹, Jianhua Wang¹, Mulin Jun Li^{1

3}

Affiliations

¹ Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
² School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, China.
³ Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.

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