File Download
  Links for fulltext
     (May Require Subscription)
Supplementary

Article: ChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

TitleChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
Authors
Issue Date2011
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic Acids Research, 2011, v. 39 SUPPL. 2, p. W430-W436 How to Cite?
AbstractChromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-Array, with free access to academic users. © 2011 The Author(s).
Persistent Identifierhttp://hdl.handle.net/10722/138953
ISSN
2015 Impact Factor: 9.202
2015 SCImago Journal Rankings: 7.458
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
University of Hong Kong
Centre for Reproduction Development and Growth of The University of Hong Kong
Research Grants Council of Hong Kong778609M
N_HKU752/10
National Natural Science Foundation of China
Funding Information:

University Postgraduate Fellowship [to J.Q.] from The University of Hong Kong; Centre for Reproduction Development and Growth of The University of Hong Kong [start up fund to J.W.]; General Research Fund [grant number 778609M to J.W.] from the Research Grants Council of Hong Kong; The National Natural Science Foundation of China and Research Grants Council of Hong Kong Joint Research Scheme [grant number N_HKU752/10 to J.W. and M. Q.Z.]. Funding for open access charge: General Research Fund [grant number 778609M to J.W.] from the Research Grants Council of Hong Kong.

References

 

DC FieldValueLanguage
dc.contributor.authorQin, Jen_HK
dc.contributor.authorLi, MJen_HK
dc.contributor.authorWang, Pen_HK
dc.contributor.authorZhang, MQen_HK
dc.contributor.authorWang, Jen_HK
dc.date.accessioned2011-09-23T05:43:03Z-
dc.date.available2011-09-23T05:43:03Z-
dc.date.issued2011en_HK
dc.identifier.citationNucleic Acids Research, 2011, v. 39 SUPPL. 2, p. W430-W436en_HK
dc.identifier.issn0305-1048en_HK
dc.identifier.urihttp://hdl.handle.net/10722/138953-
dc.description.abstractChromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-Array, with free access to academic users. © 2011 The Author(s).en_HK
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/en_HK
dc.relation.ispartofNucleic Acids Researchen_HK
dc.subject.meshChromatin Immunoprecipitation-
dc.subject.meshGene Expression Profiling-
dc.subject.meshOligonucleotide Array Sequence Analysis-
dc.subject.meshSoftware-
dc.subject.meshTranscription Factors - metabolism-
dc.titleChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factoren_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0305-1048&volume=39, suppl. 2&spage=W430&epage=W436&date=2011&atitle=ChIP-Array:+combinatory+analysis+of+ChIP-seq/chip+and+microarray+gene+expression+data+to+discover+direct/indirect+targets+of+a+transcription+factor-
dc.identifier.emailWang, J:junwen@hkucc.hku.hken_HK
dc.identifier.authorityWang, J=rp00280en_HK
dc.description.naturepublished_or_final_versionen_US
dc.identifier.doi10.1093/nar/gkr332en_HK
dc.identifier.pmid21586587en_HK
dc.identifier.pmcidPMC3125757-
dc.identifier.scopuseid_2-s2.0-79959930131en_HK
dc.identifier.hkuros192076en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79959930131&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume39en_HK
dc.identifier.issueSUPPL. 2en_HK
dc.identifier.spageW430en_HK
dc.identifier.epageW436en_HK
dc.identifier.eissn1362-4962-
dc.identifier.isiWOS:000292325300070-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.f100010960956-
dc.identifier.scopusauthoridQin, J=54397721700en_HK
dc.identifier.scopusauthoridLi, MJ=37008547900en_HK
dc.identifier.scopusauthoridWang, P=54397871300en_HK
dc.identifier.scopusauthoridZhang, MQ=35235931600en_HK
dc.identifier.scopusauthoridWang, J=8950599500en_HK
dc.identifier.citeulike9319196-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats