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Homin Lee, William Braynen, K. Keshav, P. Pavlidis (2005)
ErmineJ: Tool for functional analysis of gene expression data setsBMC Bioinformatics, 6
A. Subramanian, P. Tamayo, V. Mootha, Sayan Mukherjee, B. Ebert, Michael Gillette, A. Paulovich, S. Pomeroy, T. Golub, E. Lander, J. Mesirov (2005)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profilesProceedings of the National Academy of Sciences of the United States of America, 102
Chaya Zilberstein, E. Eskin, Z. Yakhini (2004)
Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs
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.
Briefings in Bioinformatics – Oxford University Press
Published: Jun 26, 2006
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