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. 2011 May 15;27(10):1447-8.
doi: 10.1093/bioinformatics/btr156. Epub 2011 Mar 30.

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

Li Chen  1 , George Wu, Hongkai Ji
Affiliations

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

Li Chen et al. Bioinformatics. .

Abstract

hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11 069 914 protein-DNA interactions. A web server provides interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell-type dependencies, and cross-sample variability of protein-DNA interactions.

Availability: http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl.

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Figures

Fig. 1.
Fig. 1.
Illustration of hmChIP. (a) The web interface for data query and retrieval. (b) Binding intensities are retrieved and returned as text files. (c) A hierarchical clustering heat map will be returned as well. Three detailed examples and colored screen shots in larger size are provided in Supplementary Figures S1–S3.
See this image and copyright information in PMC

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