Difference between revisions of "Gsea papers"
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| − | The following papers use the GSEA / Kolmogorov-Smirnov statistics. They illustrate different applications of the methodology.<br />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]. For information on how to cite the gene set enrichment analysis, GSEA software, and/or MSigDB, see [[Gsea_Citation]].<br /><br /> 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) Proc. Natl. Acad. Sci. USA 102, 15545-15550. <strong>Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles.<br /><br /></strong> Andrea Bild and Phillip George Febbo PNAS | October 25, 2005 | vol. 102 | no. 43 | 15278-15279 <strong>COMMENTARY: Application of a priori established gene sets to discover biologically important differential expression in microarray data</strong><br /><br />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). <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 /><br />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). <strong> PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. </strong>Nat Genet<em> 34</em>, 267-273.<br /><br />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). <strong>Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response.</strong> Blood.<br /><br />Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., and Jacks, T. (2005). <strong>An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis</strong>. Nat Genet<em> 37</em>, 48-55.<br /><br />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). <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 /><br /> 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). <strong> A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility</strong> PNAS | September 13, 2005 | vol. 102 | no. 37 | 13194-13199<br /><br /> Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson. <strong> EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion � Possible Role in Nasopharyngeal Carcinoma Metastasis.</strong> Accepted Journal of Virology, 2005<br /><br />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 <strong> Altered transcriptional program of the leukemogenic transcription factor GATA1 in acute megakaryoblastic leukemia of Down Syndrome</strong> In review PNAS, 2005<br /><br /> Isakoff et al. <strong>Inactivation of the Snf5 Tumor Suppressor Stimulates Cell Cycle Progression and Cooperates with p53 Loss in Oncogenic Transformation</strong> PNAS Accepted 2005 | + | The following papers use the GSEA / Kolmogorov-Smirnov statistics. They illustrate different applications of the methodology.<br />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]. For information on how to cite the gene set enrichment analysis, GSEA software, and/or MSigDB, see [[Gsea_Citation]].<br /><br /> 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) Proc. Natl. Acad. Sci. USA 102, 15545-15550. [http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=120 <strong>Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles]. </strong><strong><br /><br /></strong> Andrea Bild and Phillip George Febbo PNAS | October 25, 2005 | vol. 102 | no. 43 | 15278-15279 <strong>COMMENTARY: Application of a priori established gene sets to discover biologically important differential expression in microarray data</strong><br /><br />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). <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 /><br />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). <strong> PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. </strong>Nat Genet<em> 34</em>, 267-273.<br /><br />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). <strong>Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response.</strong> Blood.<br /><br />Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., and Jacks, T. (2005). <strong>An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis</strong>. Nat Genet<em> 37</em>, 48-55.<br /><br />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). <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 /><br /> 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). <strong> A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility</strong> PNAS | September 13, 2005 | vol. 102 | no. 37 | 13194-13199<br /><br /> Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson. <strong> EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion � Possible Role in Nasopharyngeal Carcinoma Metastasis.</strong> Accepted Journal of Virology, 2005<br /><br />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 <strong> Altered transcriptional program of the leukemogenic transcription factor GATA1 in acute megakaryoblastic leukemia of Down Syndrome</strong> In review PNAS, 2005<br /><br /> Isakoff et al. <strong>Inactivation of the Snf5 Tumor Suppressor Stimulates Cell Cycle Progression and Cooperates with p53 Loss in Oncogenic Transformation</strong> PNAS Accepted 2005 |
Revision as of 08:52, 3 May 2006
The following papers 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. For information on how to cite the gene set enrichment analysis, GSEA software, and/or MSigDB, see Gsea_Citation.
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) Proc. Natl. Acad. Sci. USA 102, 15545-15550. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles.
Andrea Bild and Phillip George Febbo PNAS | October 25, 2005 | vol. 102 | no. 43 | 15278-15279 COMMENTARY: Application of a priori established gene sets to discover biologically important differential expression in microarray data
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.
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.
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.
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.
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.
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
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
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
