The Molecular Signatures Database Hallmark Gene Set Collection

[1]  J. Folkman,et al.  Blood Vessel Formation: What Is Its Molecular Basis? , 1996, Cell.

[2]  M. Karsy,et al.  Established and emerging variants of glioblastoma multiforme: review of morphological and molecular features. , 2012, Folia neuropathologica.

[3]  Ben S. Wittner,et al.  Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 , 2009, Nature.

[4]  S. Gabriel,et al.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.

[5]  M. Levandowsky,et al.  Distance between Sets , 1971, Nature.

[6]  Maria Keays,et al.  ArrayExpress update—trends in database growth and links to data analysis tools , 2012, Nucleic Acids Res..

[7]  Stefan Van Aelst,et al.  Fast and robust bootstrap for multivariate inference: The R package FRB , 2013 .

[8]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[9]  Takahiro Matsumoto,et al.  The androgen receptor in health and disease. , 2013, Annual review of physiology.

[10]  Stephen S. Taylor,et al.  Mitosis and apoptosis: how is the balance set? , 2013, Current opinion in cell biology.

[11]  Scott L. Pomeroy,et al.  Medulloblastomics: the end of the beginning , 2012, Nature Reviews Cancer.

[12]  Daniel Müllner,et al.  fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python , 2013 .

[13]  J. Mesirov,et al.  Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[14]  Bradley Efron,et al.  Large-scale inference , 2010 .

[15]  Jill P. Mesirov,et al.  Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data , 2003, Machine Learning.

[16]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2015 , 2014, Nucleic Acids Res..

[17]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[18]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[19]  A. Hata,et al.  Targeting the TGFβ signalling pathway in disease , 2012, Nature Reviews Drug Discovery.

[20]  Allan Birnbaum,et al.  Combining Independent Tests of Significance , 1954 .

[21]  J. Barnholtz-Sloan,et al.  CBTRUS statistical report: primary brain and central nervous system tumors diagnosed in the United States in 2007-2011. , 2012, Neuro-oncology.

[22]  J. Darnell,et al.  The JAK-STAT pathway at twenty. , 2012, Immunity.

[23]  Raghu Kalluri,et al.  The basics of epithelial-mesenchymal transition. , 2009, The Journal of clinical investigation.

[24]  Pablo Tamayo,et al.  Metagenes and molecular pattern discovery using matrix factorization , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  S. Nishizuka,et al.  Reverse-phase protein lysate microarrays for cell signaling analysis , 2008, Nature Protocols.

[26]  Dennis B. Troup,et al.  NCBI GEO: mining tens of millions of expression profiles—database and tools update , 2006, Nucleic Acids Res..

[27]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Yan Lin,et al.  An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection , 2012, Bioinform..

[29]  P. Good.  Analyzing the Large Number of Variables in Biomedical Imagery: A Brief Review , 2011, Journal of biopharmaceutical statistics.

[30]  E. Neilson,et al.  Biomarkers for epithelial-mesenchymal transitions. , 2009, The Journal of clinical investigation.

[31]  Allard Kaptein,et al.  Dominant Negative Stat3 Mutant Inhibits Interleukin-6-induced Jak-STAT Signal Transduction (*) , 1996, The Journal of Biological Chemistry.

[32]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[33]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[34]  G. Ferbeyre,et al.  The role of Stat5 transcription factors as tumor suppressors or oncogenes. , 2011, Biochimica et biophysica acta.

[35]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .