StripeDiff: Model-based algorithm for differential analysis of chromatin stripe

Krishan Gupta, Guangyu Wang, Shuo Zhang, Xinlei Gao, Rongbin Zheng, Yanchun Zhang, Qingshu Meng, Lili Zhang, Qi Cao, Kaifu Chen

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Multiple recent studies revealed stripes as an architectural feature of three-dimensional chromatin and found stripes connected to epigenetic regulation of transcription. Whereas a couple of tools are available to define stripes in a single sample, there is yet no reported method to quantitatively measure the dynamic change of each stripe between samples. Here,we developed StripeDiff, a bioinformatics tool that delivers a set of statistical methods to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to 12 sets of Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation. StripeDiff will be a robust tool for the community to facilitate understanding of stripes and their function in numerous biological models.

Original languageEnglish (US)
Article numberabk2246
JournalScience Advances
Volume8
Issue number49
DOIs
StatePublished - 2022

ASJC Scopus subject areas

  • General

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