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Circumventing the cut-off for enrichment analysis

Circumventing the cut-off for enrichment analysis Three tools for threshold-free enrichment analysis of microarray data are introduced: GSEA (gene set enrichment analysis), ermineJ and DRIM (discovering rank imbalanced motifs). GSEA offers an interface to a specific algorithm and a well-defined pipeline for the identifying enrichment in diverse gene sets and the creation of signature profiles. ermineJ offers a combined front end to three different algorithms, two of which perform a cut-off-free enrichment analysis. DRIM comprises an implementation of a new algorithm and is specifically designed for the search of new transcription-factor-binding sites based on expression patterns. Together, these tools demonstrate an emerging trend in high-throughput data analysis—the joint analysis of raw results with external knowledge. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Briefings in Bioinformatics Oxford University Press

Circumventing the cut-off for enrichment analysis

Briefings in Bioinformatics , Volume 7 (2) – Jun 26, 2006

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References (3)

Publisher
Oxford University Press
Copyright
© Published by Oxford University Press.
ISSN
1467-5463
eISSN
1477-4054
DOI
10.1093/bib/bbl013
Publisher site
See Article on Publisher Site

Abstract

Three tools for threshold-free enrichment analysis of microarray data are introduced: GSEA (gene set enrichment analysis), ermineJ and DRIM (discovering rank imbalanced motifs). GSEA offers an interface to a specific algorithm and a well-defined pipeline for the identifying enrichment in diverse gene sets and the creation of signature profiles. ermineJ offers a combined front end to three different algorithms, two of which perform a cut-off-free enrichment analysis. DRIM comprises an implementation of a new algorithm and is specifically designed for the search of new transcription-factor-binding sites based on expression patterns. Together, these tools demonstrate an emerging trend in high-throughput data analysis—the joint analysis of raw results with external knowledge.

Journal

Briefings in BioinformaticsOxford University Press

Published: Jun 26, 2006

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