Broad Institute of MIT and Harvard

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2008

Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells, Mishra, P.J.; Mishra, P.J.; Humeniuk, R.; Medina, D.J.; Alexe, G.; Mesirov, J.P.; Ganesan, S.; Glod, J.W.; Banerjee, D. , Cancer Research, 2008/06/01/, Volume 68, Issue 11, p.4331 - 9, (2008) Abstract
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Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases, Xu, L.; Shen, S.S.; Hoshida, Y.; Subramanian, A.; Ross, K.; Brunet, J.; Wagner, S.N.; Ramaswamy, S.; Mesirov, J.P.; Hynes, R.O. , Molecular Cancer Research: MCR, 2008/05//, Volume 6, Issue 5, p.760 - 9, (2008) Abstract
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Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases, Lei Xu, S.S.S.; Hynes, R.O. , Volume 6, Issue May 1, p.760-769, (2008) Abstract
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2007

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates, Alexe, G.; Dalgin, G.S.; Scanfeld, D.; Tamayo, P.; Mesirov, J.P.; DeLisi, C.; Harris, L.; Barnard, N.; Martel, M.; Levine, A.J.; Ganesan, S.; Bhanot, G. , Cancer Research, 2007/11/15/, Volume 67, Issue 22, p.10669 - 76, (2007) Abstract
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Metagene projection for cross-platform, cross-species characterization of global transcriptional states, Tamayo, P.; Scanfeld, D.; Ebert, B.L.; Gillette, M.A.; Roberts, C.W.M.; Mesirov, J.P. , Proceedings of the National Academy of Sciences of the United States of America, 2007/04/03/, Volume 104, Issue 14, p.5959 - 64, (2007) Abstract
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Portraits of breast cancer progression, Dalgin, G.S.; Alexe, G.; Scanfeld, D.; Tamayo, P.; Mesirov, J.P.; Ganesan, S.; DeLisi, C.; Bhanot, G. , BMC Bioinformatics, 2007///, Volume 8, p.291 - 291, (2007) Abstract
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Subclass mapping: identifying common subtypes in independent disease data sets, Hoshida, Y.; Brunet, J.; Tamayo, P.; Golub, T.R.; Mesirov, J.P. , PLoS ONE, 2007///, Volume 2, Issue 11, p.e1195 - e1195, (2007) Abstract
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2006

Comparative gene marker selection suite, Gould, J.; Getz, G.; Monti, S.; Reich, M.; Mesirov, J.P. , Bioinformatics (Oxford, England), 2006/08/01/, Volume 22, Issue 15, p.1924 - 5, (2006) Abstract
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GenePattern 2.0, Reich, M.; Liefeld, T.; Gould, J.; Lerner, J.; Tamayo, P.; Mesirov, J.P. , Nature Genetics, 2006/05//, Volume 38, Issue 5, p.500 - 1, (2006)
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2005

Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation, Isakoff, M.S.; Sansam, C.G.; Tamayo, P.; Subramanian, A.; Evans, J.A.; Fillmore, C.M.; Wang, X.; Biegel, J.A.; Pomeroy, S.L.; Mesirov, J.P.; Roberts, C.W.M. , Proceedings of the National Academy of Sciences of the United States of America, 2005/12/06/, Volume 102, Issue 49, p.17745 - 50, (2005) Abstract
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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, 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. , Proceedings of the National Academy of Sciences of the United States of America, 2005/10/25/, Volume 102, Issue 43, p.15545 - 50, (2005) Abstract
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GeneCruiser: a web service for the annotation of microarray data, Liefeld, T.; Reich, M.; Gould, J.; Zhang, P.; Tamayo, P.; Mesirov, J.P. , Bioinformatics (Oxford, England), 2005/09/15/, Volume 21, Issue 18, p.3681 - 2, (2005) Abstract
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An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis, Sweet-Cordero, A.; Mukherjee, S.; Subramanian, A.; You, H.; Roix, J.J.; Ladd-Acosta, C.; Mesirov, J.; Golub, T.R.; Jacks, T. , Nature Genetics, 2005/01//, Volume 37, Issue 1, p.48 - 55, (2005) Abstract
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2004

GeneCluster 2.0: an advanced toolset for bioarray analysis, Reich, M.; Ohm, K.; Angelo, M.; Tamayo, P.; Mesirov, J.P. , Bioinformatics (Oxford, England), 2004/07/22/, Volume 20, Issue 11, p.1797 - 8, (2004) Abstract
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Metagenes and molecular pattern discovery using matrix factorization, Brunet, J.; Tamayo, P.; Golub, T.R.; Mesirov, J.P. , Proceedings of the National Academy of Sciences of the United States of America, 2004/03/23/, Volume 101, Issue 12, p.4164 - 9, (2004) Abstract
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Supplemental Materials
Files Paper Figures Supplement Classics Res File Classics Class File NonClassics Res File NonClassics Class File CEL Files Files Manuscript (PDF) Supplementary Information document (MS Word) Figures (MS Power Point) Datasets and clinical table (ZIP, 13 Mbytes) Sample list Raw data 1/4 (57 MB) Raw data 2/4 (57 MB) (57 MB) Raw data 3/4 (58 MB) (57 MB) Raw data 4/4 (58 MB) Dataset C (gene expression) RES file format Dataset C (class labels) CLS file format Dataset C (clinical table) ASCII file format Files Supplementary Appendix 1 Supplementary Figure A4-1 Supplementary Figure A6-1 Supplementary Figure A6-2 Supplementary Figure A2-1 Supplementary Table 1 Supplementary Table 2 Supplementary Table 3a Supplementary Table 3b Files Supplementary Information URLs Medical News Today URLs Blood Highlight Files Manuscript Figures References Raw data (mean scaled, see supplement) Raw data (unscaled) Sample annotation 2118 genes (Top 5% by F statistic) 4246 genes (Top 10% by F statistic) ASH meeting presentation (slides) ASH meeting presentation (handouts) UNIGENE and GenBank annotation of Affymetrix UNIGENE and GenBank annotation of Lymphochip Lymphochip 2 Affymetrix mapping Consensus Clusters' Markers URLs PNAS Supplemental Information Files PGC-1-alpha timecourse (scaled expression data) Mouse promoters Mouse:human masked promoters Gene list for Figure 1 correlogram Files Technical Report Leukemia data Leukemia class template Novartis multi-tissue data Novartis multi-tissue class template St. Jude Leukemia data St. Jude Leukemia class template Lung cancer data Lung cancer class template CNS tumors data CNS tumors class template Normal tissues data Normal tissues class template Uniform1 Gaussian1 Gaussian3 Gaussian3 class template Gaussian4 Gaussian4 class template Gaussian5.delta2 Gaussian5.delta3 Gaussian5 class template Simulated6 Simulated6 class template URLs Same datasets as this paper Files Paper (Word document) URLs Multi-tumor Cancer Map Paper Lung Paper Breast Paper Prostate Paper Medulloblastoma Paper Lymphoma Paper Files Manuscript Supplement Supplemental Information Dataset A - Global Cancer Map Tumor vs. Met. Dataset B - Lung Outcome Dataset C - Rosetta Breast Outcome Dataset D - Prostate Outcome Dataset E - Medulloblastoma Outcome Dataset F - LBC Lymphoma Outcome Table of Contents

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