PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular re...

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Bibliographic Details
Published in:Nucleic acids research 2009-01, Vol.37 (suppl-1), p.D54-D60
Main Authors: Portales-Casamar, Elodie, Arenillas, David, Lim, Jonathan, Swanson, Magdalena I, Jiang, Steven, McCallum, Anthony, Kirov, Stefan, Wasserman, Wyeth W
Format: Article
Language:English
Subjects:
Base Sequence
Binding Sites
Conserved Sequence
Databases, Genetic
Gene Expression Regulation
Regulatory Elements, Transcriptional
Sequence Alignment
Sequence Analysis, DNA
Software
Transcription Factors - metabolism
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Summary:The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data 'boutiques' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkn783