Circumventing the cut-off for enrichment analysis

by: Eitan Rubin

Brief Bioinform, Vol. 7, No. 2. (1 June 2006), pp. 202-203.

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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. 10.1093/bib/bbl013

@article{citeulike:2801344, 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. 10.1093/bib/bbl013}, author = {Rubin, Eitan }, citeulike-article-id = {2801344}, doi = {10.1093/bib/bbl013}, journal = {Brief Bioinform}, keywords = {gene\_sets}, month = {June}, number = {2}, pages = {202--203}, posted-at = {2008-05-15 12:21:22}, priority = {2}, title = {Circumventing the cut-off for enrichment analysis}, url = {http://dx.doi.org/10.1093/bib/bbl013}, volume = {7}, year = {2006} }

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TY - JOUR ID - citeulike:2801344 L3 - citeulike-article-id:2801344 TI - Circumventing the cut-off for enrichment analysis JF - Brief Bioinform VL - 7 IS - 2 SP - 202 EP - 203 N2 - 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. 10.1093/bib/bbl013 KW - gene_sets AU - Rubin, Eitan PY - 2006/06/01/ UR - http://dx.doi.org/10.1093/bib/bbl013 ER -

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