Gene-set enrichment analysis

Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, MA., Paulovich, A., Pomeroy, S.L., Golub, T.IL, Lander, E.S., et al, (2005) Gene Set Enrichment Analysis A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles. Proc Natl Acad Sci USA, 102, 15545-15550. 

Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102 15545-15550... 

The above ad hoc methods are illustrated with real data in Section 4.4. In addition to the methods described above, many other methods have been developed some of them have been compared to provide guidelines in these references (Dudoit et al., 2002 Kim et al., 2006 Kooperberg et al, 2(X)5). Scores computed from the above test can also be used for gene set enrichment analysis (GSEA) (Elion and Tibshirani, 2007 Jiang and Gentleman, 2007 Subramanian et al., 2005 Tian et al., 2005), which analyzes the data of a predefined set of genes. 

Oh SJ, Ahn JY, Chung DH. Comparison of invariant NKT cells with conventional T cells by using gene set enrichment analysis (GSEA). Immune New. 2011 11 406-11. 

Subramanian A., Kuehn H., Gould J., et al. 2007. GSEA-P a desktop appUeation for gene set enrichment analysis. Bioinformatics 23(23) 3251-3253. 

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