ChIP-Array 2: Integrating multiple omics data to construct gene regulatory networks

Panwen Wang, Jing Qin, Yiming Qin, Yun Zhu, Lily Yan Wang, Mulin Jun Li, Michael Q. Zhang, Junwen Wang

Research output: Contribution to journalArticle

12 Scopus citations

Abstract

Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cisregulatory elements form a complex gene transcription apparatus. Our previous work, ChIP-Array, combined TF binding and transcriptome data to construct gene regulatory networks (GRNs). Here we present an enhanced version, ChIP-Array 2, to integrate additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components. Moreover, we substantially extended our motif database for human, mouse, rat, fruit fly, worm, yeast and Arabidopsis, and curated large amount of omics data for users to select as input or backend support. With ChIP-Array 2, we compiled a library containing regulatory networks of 18 TFs/chromatin modifiers in mouse embryonic stem cell (mESC). The web server and the mESC library are publicly free and accessible at http://jjwanglab.org/chip-array.

Original languageEnglish (US)
Pages (from-to)W264-W269
JournalNucleic acids research
Volume43
Issue numberW1
DOIs
StatePublished - 2015

ASJC Scopus subject areas

  • Genetics

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    Wang, P., Qin, J., Qin, Y., Zhu, Y., Wang, L. Y., Li, M. J., Zhang, M. Q., & Wang, J. (2015). ChIP-Array 2: Integrating multiple omics data to construct gene regulatory networks. Nucleic acids research, 43(W1), W264-W269. https://doi.org/10.1093/nar/gkv398