oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

Abstract oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with...

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Bibliographic Details
Published in:G3 : genes - genomes - genetics 2012-09, Vol.2 (9), p.987-1002
Main Authors: Kwon, Andrew T, Arenillas, David J, Hunt, Rebecca Worsley, Wasserman, Wyeth W
Format: Article
Language:English
Subjects:
Animals
Base Composition
Binding Sites
Chromatin Immunoprecipitation
Cilia - genetics
Computational Biology - methods
High-Throughput Nucleotide Sequencing
Humans
Internet
Investigations
Muscle, Skeletal - metabolism
Nematoda - genetics
Nucleotide Motifs
Regulatory Sequences, Nucleic Acid
Software
Transcription Factors - metabolism
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Description
Summary:Abstract oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with known sets of co-regulated genes and published ChIP-Seq data demonstrates the capacity for oPOSSUM-3 to identify mediating transcription factors (TF) for co-regulated genes or co-recovered sequences. oPOSSUM-3 is available at http://opossum.cisreg.ca.
ISSN:2160-1836
2160-1836
DOI:10.1534/g3.112.003202