BloodChIP: A database of comparative genome-wide transcription factor binding profiles in human blood cells

Chacon, D; Beck, D; Perera, D; Wong, JWH; Pimanda, JE

BloodChIP: A database of comparative genome-wide transcription factor binding profiles in human blood cells

Chacon, D

Beck, D Perera, D Wong, JWH Pimanda, JE

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Publication Type:: Journal Article
Citation:: Nucleic Acids Research, 2014, 42 (D1)
Issue Date:: 2014-01-01

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Field	Value	Language
dc.contributor.author	Chacon, D https://orcid.org/0000-0003-3729-1385	en_US
dc.contributor.author	Beck, D	en_US
dc.contributor.author	Perera, D	en_US
dc.contributor.author	Wong, JWH	en_US
dc.contributor.author	Pimanda, JE	en_US
dc.date.issued	2014-01-01	en_US
dc.identifier.citation	Nucleic Acids Research, 2014, 42 (D1)	en_US
dc.identifier.issn	0305-1048	en_US
dc.identifier.uri	http://hdl.handle.net/10453/116254
dc.description.abstract	The BloodChIP database (http://www.med.unsw.edu.au/CRCWeb.nsf/page/ BloodChIP) supports exploration and visualization of combinatorial transcription factor (TF) binding at a particular locus in human CD34-positive and other normal and leukaemic cells or retrieval of target gene sets for user-defined combinations of TFs across one or more cell types. Increasing numbers of genome-wide TF binding profiles are being added to public repositories, and this trend is likely to continue. For the power of these data sets to be fully harnessed by experimental scientists, there is a need for these data to be placed in context and easily accessible for downstream applications. To this end, we have built a user-friendly database that has at its core the genome-wide binding profiles of seven key haematopoietic TFs in human stem/progenitor cells. These binding profiles are compared with binding profiles in normal differentiated and leukaemic cells. We have integrated these TF binding profiles with chromatin marks and expression data in normal and leukaemic cell fractions. All queries can be exported into external sites to construct TF-gene and protein-protein networks and to evaluate the association of genes with cellular processes and tissue expression. © 2013 The Author(s). Published by Oxford University Press.	en_US
dc.relation.ispartof	Nucleic Acids Research	en_US
dc.relation.isbasedon	10.1093/nar/gkt1036	en_US
dc.subject.classification	Developmental Biology	en_US
dc.subject.mesh	Blood Cells	en_US
dc.subject.mesh	Hematopoietic Stem Cells	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Transcription Factors	en_US
dc.subject.mesh	DNA	en_US
dc.subject.mesh	Chromatin Immunoprecipitation	en_US
dc.subject.mesh	Gene Expression Profiling	en_US
dc.subject.mesh	Binding Sites	en_US
dc.subject.mesh	Genome, Human	en_US
dc.subject.mesh	Internet	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Databases, Genetic	en_US
dc.subject.mesh	Regulatory Elements, Transcriptional	en_US
dc.title	BloodChIP: A database of comparative genome-wide transcription factor binding profiles in human blood cells	en_US
dc.type	Journal Article
utslib.citation.volume	D1	en_US
utslib.citation.volume	42	en_US
utslib.for	080301 Bioinformatics Software	en_US
utslib.for	05 Environmental Sciences	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology/School of Biomedical Engineering
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology/School of Software
pubs.organisational-group	/University of Technology Sydney/Strength - AAI - Advanced Analytics Institute Research Centre
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
utslib.copyright.status	open_access
pubs.issue	D1	en_US
pubs.publication-status	Published	en_US
pubs.volume	42	en_US

Abstract:

The BloodChIP database (http://www.med.unsw.edu.au/CRCWeb.nsf/page/ BloodChIP) supports exploration and visualization of combinatorial transcription factor (TF) binding at a particular locus in human CD34-positive and other normal and leukaemic cells or retrieval of target gene sets for user-defined combinations of TFs across one or more cell types. Increasing numbers of genome-wide TF binding profiles are being added to public repositories, and this trend is likely to continue. For the power of these data sets to be fully harnessed by experimental scientists, there is a need for these data to be placed in context and easily accessible for downstream applications. To this end, we have built a user-friendly database that has at its core the genome-wide binding profiles of seven key haematopoietic TFs in human stem/progenitor cells. These binding profiles are compared with binding profiles in normal differentiated and leukaemic cells. We have integrated these TF binding profiles with chromatin marks and expression data in normal and leukaemic cell fractions. All queries can be exported into external sites to construct TF-gene and protein-protein networks and to evaluate the association of genes with cellular processes and tissue expression. © 2013 The Author(s). Published by Oxford University Press.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/116254