TY - JOUR AU - Khatri, P. AU - Sirota, M. AU - Butte, A. J. PY - 2012 DA - 2012// TI - Ten years of pathway analysis: current approaches and outstanding challenges JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002375 DO - 10.1371/journal.pcbi.1002375 ID - Khatri2012 ER - TY - JOUR AU - Hung, J. H. AU - Yang, T. H. AU - Hu, Z. AU - Weng, Z. AU - Delisi, C. PY - 2012 DA - 2012// TI - Gene set enrichment analysis: performance evaluation and usage guidelines JO - Brief Bioinform VL - 13 UR - https://doi.org/10.1093/bib/bbr049 DO - 10.1093/bib/bbr049 ID - Hung2012 ER - TY - JOUR AU - Allison, D. B. AU - Cui, X. AU - Page, G. P. AU - Sabripour, M. PY - 2006 DA - 2006// TI - Microarray data analysis: from disarray to consolidation and consensus JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1749 DO - 10.1038/nrg1749 ID - Allison2006 ER - TY - JOUR AU - Subramanian, A. AU - Tamayo, P. AU - Mootha, V. K. AU - Mukherjee, S. AU - Ebert, B. L. AU - Gillette, M. A. AU - Paulovich, A. AU - Pomeroy, S. L. AU - Golub, T. R. AU - Lander, E. S. AU - Mesirov, J. P. PY - 2005 DA - 2005// TI - Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles JO - Proc Nat Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0506580102 DO - 10.1073/pnas.0506580102 ID - Subramanian2005 ER - TY - JOUR AU - Goeman, J. J. AU - Buehlmann, P. PY - 2007 DA - 2007// TI - Analyzing gene expression data in terms of gene sets: methodological issues JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm051 DO - 10.1093/bioinformatics/btm051 ID - Goeman2007 ER - TY - JOUR PY - 2010 DA - 2010// TI - The gene ontology in 2010: extensions and refinements JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp1018 DO - 10.1093/nar/gkp1018 ID - ref6 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. PY - 2000 DA - 2000// TI - KEGG: kyoto encyclopedia of genes and genomes JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.27 DO - 10.1093/nar/28.1.27 ID - Kanehisa2000 ER - TY - JOUR AU - Liberzon, A. AU - Subramanian, A. AU - Pinchback, R. AU - Thorvaldsdóttir, H. AU - Tamayo, P. AU - Mesirov, J. P. PY - 2011 DA - 2011// TI - Molecular signatures database (msigdb) 3.0 JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr260 DO - 10.1093/bioinformatics/btr260 ID - Liberzon2011 ER - TY - JOUR AU - Efron, B. AU - Tibshirani, R. PY - 2007 DA - 2007// TI - On testing the significance of sets of genes JO - Ann Appl Stat VL - 1 UR - https://doi.org/10.1214/07-AOAS101 DO - 10.1214/07-AOAS101 ID - Efron2007 ER - TY - JOUR AU - Barry, W. T. AU - Nobel, A. B. AU - Wright, F. A. PY - 2008 DA - 2008// TI - A statistical framework for testing functional categories in microarray data JO - Ann Appl Stat VL - 2 UR - https://doi.org/10.1214/07-AOAS146 DO - 10.1214/07-AOAS146 ID - Barry2008 ER - TY - JOUR AU - Wu, D. AU - Smyth, G. K. PY - 2012 DA - 2012// TI - Camera: a competitive gene set test accounting for inter-gene correlation JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks461 DO - 10.1093/nar/gks461 ID - Wu2012 ER - TY - JOUR AU - Zhou, Y. H. AU - Barry, W. T. AU - Wright, F. A. PY - 2013 DA - 2013// TI - Empirical pathway analysis, without permutation JO - Biostatistics VL - 14 UR - https://doi.org/10.1093/biostatistics/kxt004 DO - 10.1093/biostatistics/kxt004 ID - Zhou2013 ER - TY - JOUR AU - Tian, L. AU - Greenberg, S. A. AU - Kong, S. W. AU - Altschuler, J. AU - Kohane, I. S. AU - Park, P. J. PY - 2005 DA - 2005// TI - Discovering statistically significant pathways in expression profiling studies JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0506577102 DO - 10.1073/pnas.0506577102 ID - Tian2005 ER - TY - JOUR AU - Genovese, C. R. AU - Roeder, K. AU - Wasserman, L. PY - 2006 DA - 2006// TI - False discovery control with p-value weighting JO - Biometrika VL - 93 UR - https://doi.org/10.1093/biomet/93.3.509 DO - 10.1093/biomet/93.3.509 ID - Genovese2006 ER - TY - JOUR AU - Frost, H. R. AU - Li, Z. AU - Moore, J. H. PY - 2015 DA - 2015// TI - Spectral gene set enrichment (SGSE) JO - BMC Bioinformatics VL - 16 UR - https://doi.org/10.1186/s12859-015-0490-7 DO - 10.1186/s12859-015-0490-7 ID - Frost2015 ER - TY - JOUR AU - Frost, H. R. AU - Li, Z. AU - Moore, J. H. PY - 2015 DA - 2015// TI - Principal component gene set enrichment (PCGSE) JO - BioData Min VL - 8 UR - https://doi.org/10.1186/s13040-015-0059-z DO - 10.1186/s13040-015-0059-z ID - Frost2015 ER - TY - JOUR AU - Johnstone, I. M. PY - 2001 DA - 2001// TI - On the distribution of the largest eigenvalue in principal components analysis JO - Ann Stat VL - 29 UR - https://doi.org/10.1214/aos/1009210544 DO - 10.1214/aos/1009210544 ID - Johnstone2001 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc. Series B (Statistical Methodology) VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Bourgon, R. AU - Gentleman, R. AU - Huber, W. PY - 2010 DA - 2010// TI - Independent filtering increases detection power for high-throughput experiments JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0914005107 DO - 10.1073/pnas.0914005107 ID - Bourgon2010 ER - TY - JOUR AU - Murcray, C. E. AU - Lewinger, J. P. AU - Conti, D. V. AU - Thomas, D. C. AU - Gauderman, W. J. PY - 2011 DA - 2011// TI - Sample size requirements to detect gene-environment interactions in genome-wide association studies JO - Genet Epidemiol VL - 35 UR - https://doi.org/10.1002/gepi.20569 DO - 10.1002/gepi.20569 ID - Murcray2011 ER - TY - JOUR AU - Dai, J. Y. AU - Kooperberg, C. AU - Leblanc, M. AU - Prentice, R. L. PY - 2012 DA - 2012// TI - Two-stage testing procedures with independent filtering for genome-wide gene-environment interaction JO - Biometrika VL - 99 UR - https://doi.org/10.1093/biomet/ass044 DO - 10.1093/biomet/ass044 ID - Dai2012 ER - TY - JOUR AU - Hsu, L. AU - Jiao, S. AU - Dai, J. Y. AU - Hutter, C. AU - Peters, U. AU - Kooperberg, C. PY - 2012 DA - 2012// TI - Powerful cocktail methods for detecting genome-wide gene-environment interaction JO - Genet Epidemiol VL - 36 UR - https://doi.org/10.1002/gepi.21610 DO - 10.1002/gepi.21610 ID - Hsu2012 ER - TY - JOUR AU - Frost, H. R. AU - Andrew, A. S. AU - Karagas, M. R. AU - Moore, J. H. PY - 2015 DA - 2015// TI - A screening-testing approach for detecting gene-environment interactions using sequential penalized and unpenalized multiple logistic regression JO - Pac Symp Biocomput VL - 20 ID - Frost2015 ER - TY - JOUR AU - Frost, H. R. AU - Li, Z. AU - Asselbergs, F. W. AU - Moore, J. H. PY - 2015 DA - 2015// TI - An independent filter for gene set testing based on spectral enrichment JO - Comput Biol Bioinformatics, IEEE/ACM Trans VL - PP ID - Frost2015 ER - TY - JOUR AU - Segal, E. AU - Friedman, N. AU - Koller, D. AU - Regev, A. PY - 2004 DA - 2004// TI - A module map showing conditional activity of expression modules in cancer JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1434 DO - 10.1038/ng1434 ID - Segal2004 ER - TY - JOUR AU - Robinson, M. D. AU - Grigull, J. AU - Mohammad, N. AU - Hughes, T. R. PY - 2002 DA - 2002// TI - Funspec: a web-based cluster interpreter for yeast JO - BMC Bioinformatics VL - 3 UR - https://doi.org/10.1186/1471-2105-3-35 DO - 10.1186/1471-2105-3-35 ID - Robinson2002 ER - TY - JOUR AU - Toronen, P. PY - 2004 DA - 2004// TI - Selection of informative clusters from hierarchical cluster tree with gene classes JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-32 DO - 10.1186/1471-2105-5-32 ID - Toronen2004 ER - TY - JOUR AU - Freudenberg, J. M. AU - Joshi, V. K. AU - Hu, Z. AU - Medvedovic, M. PY - 2009 DA - 2009// TI - Clean: Clustering enrichment analysis JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-234 DO - 10.1186/1471-2105-10-234 ID - Freudenberg2009 ER - TY - JOUR AU - Choi, Y. AU - Kendziorski, C. PY - 2009 DA - 2009// TI - Statistical methods for gene set co-expression analysis JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp502 DO - 10.1093/bioinformatics/btp502 ID - Choi2009 ER - TY - JOUR AU - Rahmatallah, Y. AU - Emmert-Streib, F. AU - Glazko, G. PY - 2014 DA - 2014// TI - Gene sets net correlations analysis (gsnca): a multivariate differential coexpression test for gene sets JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt687 DO - 10.1093/bioinformatics/btt687 ID - Rahmatallah2014 ER - TY - JOUR AU - Hsueh, H. M. AU - Tsai, C. A. PY - 2016 DA - 2016// TI - Gene set analysis using sufficient dimension reduction JO - BMC Bioinformatics VL - 17 UR - https://doi.org/10.1186/s12859-016-0928-6 DO - 10.1186/s12859-016-0928-6 ID - Hsueh2016 ER - TY - BOOK AU - Mehta, M. L. PY - 2004 DA - 2004// TI - Pure and applied mathematics PB - Academic Press CY - Amsterdam ID - Mehta2004 ER - TY - JOUR AU - Johnstone, I. M. PY - 2009 DA - 2009// TI - Approximate null distribution of the largest root in multivariate analysis JO - Ann Appl Stat VL - 3 UR - https://doi.org/10.1214/08-AOAS220 DO - 10.1214/08-AOAS220 ID - Johnstone2009 ER - TY - JOUR AU - Armstrong, S. A. AU - Staunton, J. E. AU - Silverman, L. B. AU - Pieters, R. AU - den Boer, M. L. AU - Minden, M. D. AU - Sallan, S. E. AU - Lander, E. S. AU - Golub, T. R. AU - Korsmeyer, S. J. PY - 2002 DA - 2002// TI - Mll translocations specify a distinct gene expression profile that distinguishes a unique leukemia JO - Nat Genet VL - 30 UR - https://doi.org/10.1038/ng765 DO - 10.1038/ng765 ID - Armstrong2002 ER - TY - BOOK AU - Anderson, T. W. PY - 2003 DA - 2003// TI - An Introduction to Multivariate Statistical Analysis PB - Wiley-Interscience CY - Hoboken ID - Anderson2003 ER - TY - JOUR AU - Chicheportiche, R. AU - Bouchaud, J. P. PY - 2011 DA - 2011// TI - Goodness-of-fit tests with dependent observations JO - J Stat Mech: Theory Experiment VL - 2011 UR - https://doi.org/10.1088/1742-5468/2011/09/P09003 DO - 10.1088/1742-5468/2011/09/P09003 ID - Chicheportiche2011 ER - TY - JOUR AU - Patterson, N. AU - Price, A. L. AU - Reich, D. PY - 2006 DA - 2006// TI - Population structure and eigenanalysis JO - PLOS Genet VL - 2 UR - https://doi.org/10.1371/journal.pgen.0020190 DO - 10.1371/journal.pgen.0020190 ID - Patterson2006 ER - TY - JOUR AU - Soshnikov, A. PY - 2002 DA - 2002// TI - A note on universality of the distribution of the largest eigenvalues in certain sample covariance matrices JO - J Stat Phys VL - 108 UR - https://doi.org/10.1023/A:1019739414239 DO - 10.1023/A:1019739414239 ID - Soshnikov2002 ER - TY - BOOK AU - Jolliffe, I. T. PY - 2002 DA - 2002// TI - Principal Component Analysis. Springer Series in Statistics PB - Springer CY - New York ID - Jolliffe2002 ER -