TY - JOUR
T1 - ChIP-Array 2
T2 - Integrating multiple omics data to construct gene regulatory networks
AU - Wang, Panwen
AU - Qin, Jing
AU - Qin, Yiming
AU - Zhu, Yun
AU - Wang, Lily Yan
AU - Li, Mulin Jun
AU - Zhang, Michael Q.
AU - Wang, Junwen
N1 - Funding Information:
Research Grants Council, Hong Kong SAR, China [781511M, 17121414M]; National Natural Science Foundation of China, China [91229105]. Small Project Funding, University Grants Committee, The University of Hong Kong, Hong Kong SAR, China [201409176183]. Funding for open access charge: Research Grants Council, Hong Kong SAR, China [17121414M].
Funding Information:
Research Grants Council, Hong Kong SAR, China [781511M, 17121414M]; National Natural Science Foundation of China, China [91229105]. Small Project Funding, University Grants Committee, The University of Hong Kong, Hong Kong SAR, China [201409176183]. Funding for open access charge: Research Grants Council, Hong Kong SAR, China [17121414M]. Conflict of interest statement. None declared.
Publisher Copyright:
© 2015 The Author(s).
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkv398
DO - 10.1093/nar/gkv398
M3 - Article
C2 - 25916854
AN - SCOPUS:84979854771
SN - 0305-1048
VL - 43
SP - W264-W269
JO - Nucleic acids research
JF - Nucleic acids research
IS - W1
ER -