Gsea Citation
Please cite the elements of GSEA that you have used in your research.
For the gene set enrichment analysis: the analysis was first reported in Mootha et al, the Kolmogorov-Smirnov statistic was first used in the context of a set of genes in Lamb et al, and a full mathematical description of the GSEA methodology is provided in Subramanian, Tamayo, et al. To cite the gene set enrichment analysis, you may want to reference one or more these papers:
Mootha, V. K., C. M. Lindgren, et al. (2003). PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34(3): 267-73.
Lamb, J., Ramaswamy, S., Ford, H. L., Contreras, B., Martinez, R. V., Kittrell, F. S., Zahnow, C. A., Patterson, N., Golub, T. R. & Ewen, M. E. (2003). A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer. Cell 114, 323–334.
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.
To cite the Molecular Signature Database (MSigDB), whether used with GSEA or another type of analysis, please specify the MSigDB version used in your analysis and the paper that describes it. For example:
Molecular Signature Database (MSigDB), May 2006 release
--BMC paper to be released--
Note: For MSigDB releases prior to May 2006, please cite Subramanian, Tamayo, et al. (as listed above).
To cite the C3 (motif) gene sets, please reference Xie et al, as well as the Molecular Signature Database (MSigDB), as described above. For example:
Xiaohui Xie, Jun Lu, E. J. Kulbokas, Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander & Manolis Kellis. Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals. Nature 434, 17 March 2005.
Molecular Signature Database (MSigDB), May 2006 release
--BMC paper to be released--
To cite specific MSigDB gene sets, please reference the original paper on which the gene set was based, as listed in the Gene Set Card, as well as the MSigDB, as described above. For example, to cite the curated gene set ADIP_VS_PREADIP_UP:
Gerhold DL, Liu F, Jiang G, Li Z, Xu J, Lu M, Sachs JR, Bagchi A, Fridman A, Holder DJ, Doebber TW, Berger J, Elbrecht A, Moller DE, Zhang BB. Gene expression profile of adipocyte differentiation and its regulation by peroxisome proliferator-activated receptor-gamma agonists. Endocrinology 2002 Jun;143(6):2106-18.
Molecular Signature Database (MSigDB), May 2006 release
--BMC paper to be released--
To cite the GSEA software, either GSEA-P or GSEA-R, please reference the GSEA web site (http://www.broad.mit.edu/gsea/) and the Application Note paper. For example:
GSEA-P software (<a href="http://www.broad.mit.edu/gsea">http://www.broad.mit.edu/gsea</a>)
--Application Note paper to be released--
Note: Until the Application Note paper is released, please cite the URL.
