Gsea papers

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</strong>Below are selected early papers that use the GSEA / Kolmogorov-Smirnov statistics. They illustrate different applications of the methodology. For an up-to-date listing of Broad Cancer Genomics publications, click [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_menu.cgi here]. <br />
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</strong>Below are selected early papers that use the GSEA / Kolmogorov-Smirnov statistics. They illustrate different applications of the methodology. For an up-to-date listing of Broad Cancer Genomics publications, click [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_menu.cgi here]. <br />
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&nbsp;Andrea Bild and Phillip George Febbo        (2005) [http://www.pnas.org/cgi/content/extract/102/43/15278        <strong>COMMENTARY: Application of a priori established gene sets to discover biologically important            differential expression in microarray data]. </strong>PNAS | October 25, 2005 | vol. 102 | no. 43 | 15278-15279.<br />
&nbsp;Andrea Bild and Phillip George Febbo        (2005) [http://www.pnas.org/cgi/content/extract/102/43/15278        <strong>COMMENTARY: Application of a priori established gene sets to discover biologically important            differential expression in microarray data]. </strong>PNAS | October 25, 2005 | vol. 102 | no. 43 | 15278-15279.<br />
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Jean-Pierre Bourquin, Aravind Subramanian, Claudia Langebrake, Dirk Reinhardt, Olivier Bernard, Paola Ballerini, Andr&eacute; Baruchel, H&eacute;l&egrave;ne Cav&eacute;, Nicole Dastugue h, Michael Dworzak, Henrik Hasle, Gertjan L Kaspers, Michel Lessard, Lucienne Michaux, Benoit Quilichini, Paresh Vyas, Elisabeth van Wering p, Christian M Zwaan, Todd R.Golub and Stuart H. Orkin <strong> Altered transcriptional program of the leukemogenic transcription factor GATA1 in acute megakaryoblastic leukemia of Down Syndrome</strong>        . In review PNAS, 2005.<br />
Jean-Pierre Bourquin, Aravind Subramanian, Claudia Langebrake, Dirk Reinhardt, Olivier Bernard, Paola Ballerini, Andr&eacute; Baruchel, H&eacute;l&egrave;ne Cav&eacute;, Nicole Dastugue h, Michael Dworzak, Henrik Hasle, Gertjan L Kaspers, Michel Lessard, Lucienne Michaux, Benoit Quilichini, Paresh Vyas, Elisabeth van Wering p, Christian M Zwaan, Todd R.Golub and Stuart H. Orkin <strong> Altered transcriptional program of the leukemogenic transcription factor GATA1 in acute megakaryoblastic leukemia of Down Syndrome</strong>        . In review PNAS, 2005.<br />
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Isakoff et al. [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=124        <strong>Inactivation of the Snf5 Tumor Suppressor Stimulates Cell Cycle Progression and Cooperates with p53 Loss in Oncogenic Transformation</strong>].        PNAS Accepted 2005.<br />
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Isakoff et al. [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=124        <strong>Inactivation of the Snf5 Tumor Suppressor Stimulates Cell Cycle Progression and Cooperates with p53 Loss in Oncogenic Transformation</strong>].        PNAS Accepted 2005.<br />
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Lamb, J., Ramaswamy, S.,        Ford, H. L., Contreras, B., Martinez, R. V., Kittrell, F. S., Zahnow, C.        A., Patterson, N., Golub, T. R., and Ewen, M. E. (2003). [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=91 <strong>A mechanism of        cyclin D1 action encoded in the patterns of gene expression in human        cancer]. </strong>Cell<em> 114</em>, 323-334.<br />
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Lamb, J., Ramaswamy, S.,        Ford, H. L., Contreras, B., Martinez, R. V., Kittrell, F. S., Zahnow, C.        A., Patterson, N., Golub, T. R., and Ewen, M. E. (2003). [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=91 <strong>A mechanism of        cyclin D1 action encoded in the patterns of gene expression in human        cancer]. </strong>Cell<em> 114</em>, 323-334.<br />
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Justin Lamb, Emily D. Crawford, David Peck, Joshua W. Modell, Irene C. Blat, Matthew J. Wrobel, Jim Lerner, Jean-Philippe Brunet, Aravind Subramanian, Kenneth N. Ross, Michael Reich, Haley Hieronymus, Guo Wei, Scott A. Armstrong, Stephen J. Haggarty, Paul A. Clemons, Ru Wei, Steven A. Carr, Eric S. Lander, and Todd R. Golub (2006).<br />
Justin Lamb, Emily D. Crawford, David Peck, Joshua W. Modell, Irene C. Blat, Matthew J. Wrobel, Jim Lerner, Jean-Philippe Brunet, Aravind Subramanian, Kenneth N. Ross, Michael Reich, Haley Hieronymus, Guo Wei, Scott A. Armstrong, Stephen J. Haggarty, Paul A. Clemons, Ru Wei, Steven A. Carr, Eric S. Lander, and Todd R. Golub (2006).<br />
[http://www.sciencemag.org/cgi/reprint/313/5795/1929.pdf <span style="font-weight: bold;">The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease</span>]. <em>Science</em> 313: 1929-1935.<br />
[http://www.sciencemag.org/cgi/reprint/313/5795/1929.pdf <span style="font-weight: bold;">The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease</span>]. <em>Science</em> 313: 1929-1935.<br />
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Majumder, P. K., Febbo, P. G., Bikoff, R., Berger, R., Xue, Q., McMahon, L. M., Manola, J., Brugarolas, J., McDonnell, T. J., Golub, T. R.<em>, et al.</em> (2004). [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=105&nbsp; <strong> mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways].</strong> Nat Med<em>        10</em>, 594-601.<br />
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Majumder, P. K., Febbo, P. G., Bikoff, R., Berger, R., Xue, Q., McMahon, L. M., Manola, J., Brugarolas, J., McDonnell, T. J., Golub, T. R.<em>, et al.</em> (2004). [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=105&nbsp; <strong> mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways].</strong> Nat Med<em>        10</em>, 594-601.<br />
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Monti, S., Savage, K. J., Kutok, J. L., Feuerhake, F., Kurtin, P., Mihm, M., Wu, B., Pasqualucci, L., Neuberg, D., Aguiar, R. C.<em>, et al.</em> (2004). [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=102 <strong>Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response].</strong> Blood.<br />
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Monti, S., Savage, K. J., Kutok, J. L., Feuerhake, F., Kurtin, P., Mihm, M., Wu, B., Pasqualucci, L., Neuberg, D., Aguiar, R. C.<em>, et al.</em> (2004). [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=102 <strong>Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response].</strong> Blood.<br />
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Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson. [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=121 <strong> EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion � Possible Role in Nasopharyngeal Carcinoma Metastasis].</strong>        Accepted Journal of Virology, 2005<br />
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Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson. [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=121 <strong> EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion � Possible Role in Nasopharyngeal Carcinoma Metastasis].</strong>        Accepted Journal of Virology, 2005<br />
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Jennifer L. Shepard*, James F. Amatruda*, Howard M. Stern, Aravind Subramanian,        David Finkelstein, James Ziai, K. Rose Finley, Kathleen L. Pfaff, Candace Hersey, Yi Zhou,        Bruce Barut, Matthew Freedman, Charles Lee, Jan Spitsbergen, Donna Neuberg, Gerhard Weber,        Todd R. Golub, Jonathan N. Glickman, Jeffery L. Kutok, Jon C. Aster, and Leonard I. Zon        (2005). [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=111 <strong>        A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility].</strong>        PNAS | September 13, 2005 | vol. 102 | no. 37 | 13194-13199.<br />
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Jennifer L. Shepard*, James F. Amatruda*, Howard M. Stern, Aravind Subramanian,        David Finkelstein, James Ziai, K. Rose Finley, Kathleen L. Pfaff, Candace Hersey, Yi Zhou,        Bruce Barut, Matthew Freedman, Charles Lee, Jan Spitsbergen, Donna Neuberg, Gerhard Weber,        Todd R. Golub, Jonathan N. Glickman, Jeffery L. Kutok, Jon C. Aster, and Leonard I. Zon        (2005). [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=111 <strong>        A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility].</strong>        PNAS | September 13, 2005 | vol. 102 | no. 37 | 13194-13199.<br />
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Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., and Jacks, T. (2005). [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=113 <strong>An oncogenic KRAS2        expression signature identified by cross-species gene-expression analysis</strong>].        Nat Genet<em> 37</em>, 48-55.<br />
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Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., and Jacks, T. (2005). [http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&amp;paper_id=113 <strong>An oncogenic KRAS2        expression signature identified by cross-species gene-expression analysis</strong>].        Nat Genet<em> 37</em>, 48-55.<br />
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Andrew C Tolonen,  John Aach,  Debbie Lindell,  Zackary I Johnson,  Trent Rector,  Robert Steen,  George M Church and Sallie W Chisholm (2006).<br />
Andrew C Tolonen,  John Aach,  Debbie Lindell,  Zackary I Johnson,  Trent Rector,  Robert Steen,  George M Church and Sallie W Chisholm (2006).<br />
[http://www.nature.com/msb/journal/v2/n1/full/msb4100087.html Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability]. Molecular Systems Biology 2, doi:10.1038/msb4100087.
[http://www.nature.com/msb/journal/v2/n1/full/msb4100087.html Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability]. Molecular Systems Biology 2, doi:10.1038/msb4100087.

Revision as of 15:14, 16 July 2009

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Following are the GSEA papers:

Subramanian, A., Kuehn, H., Gould, J., Tamayo, P., Mesirov, J.P. (2007) GSEA-P: A desktop application for Gene Set Enrichment Analysis. Bioinformatics, doi: 10.1093/bioinformatics/btm369.

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.

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.



Below are selected early papers that use the GSEA / Kolmogorov-Smirnov statistics. They illustrate different applications of the methodology. For an up-to-date listing of Broad Cancer Genomics publications, click here.

 Andrea Bild and Phillip George Febbo (2005) COMMENTARY: Application of a priori established gene sets to discover biologically important differential expression in microarray data. PNAS | October 25, 2005 | vol. 102 | no. 43 | 15278-15279.

Jean-Pierre Bourquin, Aravind Subramanian, Claudia Langebrake, Dirk Reinhardt, Olivier Bernard, Paola Ballerini, André Baruchel, Hélène Cavé, Nicole Dastugue h, Michael Dworzak, Henrik Hasle, Gertjan L Kaspers, Michel Lessard, Lucienne Michaux, Benoit Quilichini, Paresh Vyas, Elisabeth van Wering p, Christian M Zwaan, Todd R.Golub and Stuart H. Orkin Altered transcriptional program of the leukemogenic transcription factor GATA1 in acute megakaryoblastic leukemia of Down Syndrome . In review PNAS, 2005.

Isakoff et al. Inactivation of the Snf5 Tumor Suppressor Stimulates Cell Cycle Progression and Cooperates with p53 Loss in Oncogenic Transformation. PNAS Accepted 2005.

Lamb, J., Ramaswamy, S., Ford, H. L., Contreras, B., Martinez, R. V., Kittrell, F. S., Zahnow, C. A., Patterson, N., Golub, T. R., and Ewen, M. E. (2003). A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell 114, 323-334.

Justin Lamb, Emily D. Crawford, David Peck, Joshua W. Modell, Irene C. Blat, Matthew J. Wrobel, Jim Lerner, Jean-Philippe Brunet, Aravind Subramanian, Kenneth N. Ross, Michael Reich, Haley Hieronymus, Guo Wei, Scott A. Armstrong, Stephen J. Haggarty, Paul A. Clemons, Ru Wei, Steven A. Carr, Eric S. Lander, and Todd R. Golub (2006).
The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease. Science 313: 1929-1935.

Majumder, P. K., Febbo, P. G., Bikoff, R., Berger, R., Xue, Q., McMahon, L. M., Manola, J., Brugarolas, J., McDonnell, T. J., Golub, T. R., et al. (2004). mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways. Nat Med 10, 594-601.

Monti, S., Savage, K. J., Kutok, J. L., Feuerhake, F., Kurtin, P., Mihm, M., Wu, B., Pasqualucci, L., Neuberg, D., Aguiar, R. C., et al. (2004). Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood.


Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson. EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion � Possible Role in Nasopharyngeal Carcinoma Metastasis. Accepted Journal of Virology, 2005

Jennifer L. Shepard*, James F. Amatruda*, Howard M. Stern, Aravind Subramanian, David Finkelstein, James Ziai, K. Rose Finley, Kathleen L. Pfaff, Candace Hersey, Yi Zhou, Bruce Barut, Matthew Freedman, Charles Lee, Jan Spitsbergen, Donna Neuberg, Gerhard Weber, Todd R. Golub, Jonathan N. Glickman, Jeffery L. Kutok, Jon C. Aster, and Leonard I. Zon (2005). A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility. PNAS | September 13, 2005 | vol. 102 | no. 37 | 13194-13199.

Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., and Jacks, T. (2005). An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 37, 48-55.

Andrew C Tolonen, John Aach, Debbie Lindell, Zackary I Johnson, Trent Rector, Robert Steen, George M Church and Sallie W Chisholm (2006).
Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Molecular Systems Biology 2, doi:10.1038/msb4100087.

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