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Nucleic Acids Res. 2014 Jan;42(Database issue):D450-8. doi: 10.1093/nar/gkt1151. Epub 2013 Nov 18.

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.

Author information

1
Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai 200092, China and Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard school of Public Health, 450 Brookline Avenue, Boston, MA 02215, USA.

Abstract

Diversified histone modifications (HMs) are essential epigenetic features. They play important roles in fundamental biological processes including transcription, DNA repair and DNA replication. Chromatin regulators (CRs), which are indispensable in epigenetics, can mediate HMs to adjust chromatin structures and functions. With the development of ChIP-Seq technology, there is an opportunity to study CR and HM profiles at the whole-genome scale. However, no specific resource for the integration of CR ChIP-Seq data or CR-HM ChIP-Seq linkage pairs is currently available. Therefore, we constructed the CR Cistrome database, available online at http://compbio.tongji.edu.cn/cr and http://cistrome.org/cr/, to further elucidate CR functions and CR-HM linkages. Within this database, we collected all publicly available ChIP-Seq data on CRs in human and mouse and categorized the data into four cohorts: the reader, writer, eraser and remodeler cohorts, together with curated introductions and ChIP-Seq data analysis results. For the HM readers, writers and erasers, we provided further ChIP-Seq analysis data for the targeted HMs and schematized the relationships between them. We believe CR Cistrome is a valuable resource for the epigenetics community.

PMID:
24253304
PMCID:
PMC3965064
DOI:
10.1093/nar/gkt1151
[Indexed for MEDLINE]
Free PMC Article

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