|
|
| (11 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| − | <p class="MsoNormal">Please cite the elements of GSEA that you have used in your research.</p> | + | <p class="MsoNormal"> </p> |
| − | <p class="MsoListNumber"><!--[if !supportLists]--><span style=""><span style=""></span></span>To cite the gene set enrichment analysis, please reference the following 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 class="MsoNormal" style="margin-left: 0.5in;">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, [http://www.broad.mit.edu/gsea/ http://www.broad.mit.edu/gsea/]).</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></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 class="MsoNormal">To cite an individual MSigDB gene set, please reference the Molecular Signature Database (MSigDB) and also the original paper or other source for the gene set (see the Gene Set Card for the gene set).<br /> |
| | + | </p> |
| | + | <p class="MsoNormal">To cite the first use of the gene set enrichment analysis:<br /> |
| | + | </p> |
| | + | <div style="margin-left: 40px;">Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E.<em>, et al.</em> (2003). [http://www.nature.com/ng/journal/v34/n3/abs/ng1180.html PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes].<strong> </strong>Nat Genet<em> 34</em>, 267-273.<br /> |
| | </div> | | </div> |
| − | <div style="font-family: arial;">
| + | <p class="MsoNormal">If you would like to redistribute the GSEA software or Molecular Signature Database (MSigDB), please contact us at mailto:gsea@broad.mit.edu.<br /> |
| − | <p class="MsoListContinue" style="margin-left: 40px;"><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.</span><br /></p> | + | </p> |
| − | <p class="MsoListContinue" style="margin-left: 40px;">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>
| |
| − | </div>
| |
| − | <div style="font-family: arial; margin-left: 40px;"> </div>
| |
| − | <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 reference the XYZ paper. For example:</p>
| |
| − | <p class="MsoListContinue" style="margin-left: 40px;">Molecular Signature Database (MSigDB), May 2006 release<br /> <paper></p>
| |
| − | <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 class="MsoListContinue" style="margin-left: 40px;">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>
| |
| − | <p class="MsoListContinue" style="margin-left: 40px;">Molecular Signature Database (MSigDB), May 2006 release<br /> <paper></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>
| |
| − | <p class="MsoListContinue" style="margin-left: 40px;">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>
| |
| − | <p class="MsoListContinue" style="margin-left: 40px;">Molecular Signature Database (MSigDB), May 2006 release<br /> <paper></p>
| |
| − | <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 XYZ paper. For example:</p>
| |
| − | <p class="MsoListContinue" style="margin-left: 40px;">GSEA-P software (<a href="http://www.broad.mit.edu/gsea">http://www.broad.mit.edu/gsea</a>)<br /> <paper></p>
| |
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, http://www.broad.mit.edu/gsea/).
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 or other source for the gene set (see the Gene Set Card for the gene set).
To cite the first use of the gene set enrichment analysis:
Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E.
, et al. (2003).
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
Nat Genet
34, 267-273.
If you would like to redistribute the GSEA software or Molecular Signature Database (MSigDB), please contact us at mailto:gsea@broad.mit.edu.
