ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.
Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cis-regulatory 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 athttp://jjwanglab.org/chip-array.
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China.
Panwen
P
Wang
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China.
Jing
J
Qin
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
Yiming
Y
Qin
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China.
Yun
Y
Zhu
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China.
Lily Yan
LY
Wang
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China.
Mulin Jun
MJ
Li
Bioinformatics Division, TNLIST, Tsinghua University, Beijing 100084, China Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Dallas, TX 75080, USA.
Michael Q
MQ
Zhang
Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China junwen@uw.edu.
Junwen
J
Wang
D000818:Animals; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D053595:Embryonic Stem Cells / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D023281:Genomics; D006657:Histones / Q000378:metabolism; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
D002843:Chromatin; D006657:Histones; D014157:Transcription Factors