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Briefings in Bioinformatics Advance Access originally published online on May 26, 2006
Briefings in Bioinformatics 2006 7(2):202-203; doi:10.1093/bib/bbl013
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

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Circumventing the cut-off for enrichment analysis

Eitan Rubin
National Institute of Biotechnology, Negev Ben Gurion University


E-mail: erubin{at}bgu.ac.il

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.


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