Chip-Array 2: Integrating Multiple Omics Data to Construct Gene Regulatory Networks

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Chip-Array 2: Integrating Multiple Omics Data to Construct Gene Regulatory Networks

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Title: Chip-Array 2: Integrating Multiple Omics Data to Construct Gene Regulatory Networks
Author(s):
Wang, Panwen;
Qin, Jing;
Qin, Yiming;
Zhu, Yun;
Wang, Lily Yan;
Li, Mulin Jun;
Zhang, Michael Q. (UT Dallas);
Wang, Junwen
Item Type: Article
Keywords: Show Keywords
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.
ISSN: 0305-1048
Persistent Link: http://hdl.handle.net/10735.1/5317
http://dx.doi.org/10.1093/nar/gkv398
Bibliographic Citation: Wang, Panwen, Jing Qin, Yiming Qin, Yun Zhu, et al. 2015. "ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks." Nucleic Acids Research 43(1), doi: 10.1093/nar/gkv398
Terms of Use: CC BY 4.0 (Attribution) License
©2015 The Authors
Sponsors: Research Grants Council (781511M, 17121414M); National Natural Science Foundation (91229105); University of Hong Kong (201409176183).

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