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| − | <p class="MsoNormal">Please cite the elements of GSEA that you have used in your research.<br /></p> | + | <p class="MsoNormal"> </p> |
| − | <p class="MsoListNumber"><!--[if !supportLists]--><span style=""><span style=""></span></span>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: </p> | + | <p class="MsoNormal">To cite the gene set enrichment analysis, GSEA software, and or the Molecular Signature Database (MSigDB):</p> |
| − | <div style="font-family: arial; margin-left: 40px;"> | + | <p style="margin-left: 0.5in;" class="MsoNormal">We acknowledge our use of the gene set enrichment analysis, GSEA software, and Molecular Signature Database (MSigDB) (Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, <a title="http://www.broad.mit.edu/gsea/" href="../../../../../../gsea/">http://www.broad.mit.edu/gsea/</a>).</p> |
| − | <p><span style="font-size: 9pt;">Mootha, V. K., C. M. Lindgren, et al. (2003). <span style="font-weight: bold;">PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.</span> Nat Genet 34(3): 267-73.<br /></span></p>
| + | <p class="MsoNormal">To cite the C3 (motif) gene sets, please reference the Molecular Signature Database (MSigDB) and also Xie et al. (2005, Nature 434).</p> |
| − | <p><span style="font-size: 9pt;">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). </span><strong>A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer.</strong><span style="font-size: 9pt;"> Cell 114, 323–334.</span><br /></p>
| + | <p class="MsoNormal">To cite an individual MSigDB gene set, please reference the Molecular Signature Database (MSigDB) and also the original paper for the gene set (see the Gene Set Card for the gene set).</p> |
| − | <p>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) <strong><strong>Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. </strong></strong>Proc. Natl. Acad. Sci. USA 102, 15545-15550.<strong> </strong> </p>
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| − | <div style="font-family: arial; margin-left: 40px;"> </div>
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| − | <p class="MsoListNumber"><!--[if !supportLists]--><span style=""><span style=""><span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->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:</p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue">Molecular Signature Database (MSigDB), May 2006 release<br />--BMC paper to be released--<br /></p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue"><span style="font-weight: bold;">Note</span>: For MSigDB releases prior to May 2006, please cite Subramanian, Tamayo, et al. (as listed above).</p>
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| − | <p class="MsoListNumber"><!--[if !supportLists]--><span style=""><span style=""></span></span>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:</p> | |
| − | <p style="margin-left: 40px;" class="MsoListContinue">Xiaohui Xie, Jun Lu, E. J. Kulbokas, Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander & Manolis Kellis. <strong style="">Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals</strong>. Nature 434, 17 March 2005.</p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue">Molecular Signature Database (MSigDB), May 2006 release<br />--BMC paper to be released--</p> | |
| − | <p class="MsoListNumber"><!--[if !supportLists]--><span style=""><span style=""><span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"></span></span></span><!--[endif]-->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:</p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue">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. <strong style="">Gene expression profile of adipocyte differentiation and its regulation by peroxisome proliferator-activated receptor-gamma agonists. </strong>Endocrinology<strong style=""> </strong>2002 Jun;143(6):2106-18.</p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue">Molecular Signature Database (MSigDB), May 2006 release<br />--BMC paper to be released--</p>
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| − | <p class="MsoListNumber"><!--[if !supportLists]--><span style=""><span style=""></span></span>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:</p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue">GSEA-P software (http://www.broad.mit.edu/gsea/)<br />--Application Note paper to be released--<br /></p>
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| − | <p style="margin-left: 40px;" class="MsoListContinue"><span style="font-weight: bold;">Note: </span>Until the Application Note paper is released, please cite the URL.<br /></p>
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To cite the gene set enrichment analysis, GSEA software, and or the Molecular Signature Database (MSigDB):
We acknowledge our use of the gene set enrichment analysis, GSEA software, and Molecular Signature Database (MSigDB) (Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, <a title="http://www.broad.mit.edu/gsea/" href="../../../../../../gsea/">http://www.broad.mit.edu/gsea/</a>).
To cite the C3 (motif) gene sets, please reference the Molecular Signature Database (MSigDB) and also Xie et al. (2005, Nature 434).
To cite an individual MSigDB gene set, please reference the Molecular Signature Database (MSigDB) and also the original paper for the gene set (see the Gene Set Card for the gene set).
