TY - JOUR AU - Luo, W. AU - Brouwer, C. PY - 2013 DA - 2013// TI - Pathview: an r/bioconductor package for pathway-based data integration and visualization JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt285 DO - 10.1093/bioinformatics/btt285 ID - Luo2013 ER - TY - JOUR AU - Bianco, L. AU - Riccadonna, S. AU - Lavezzo, E. AU - Falda, M. AU - Formentin, E. AU - Cavalieri, D. AU - Toppo, S. AU - Fontana, P. PY - 2016 DA - 2016// TI - Pathway inspector: a pathway based web application for rnaseq analysis of model and non-model organisms JO - Bioinformatics VL - 33 ID - Bianco2016 ER - TY - JOUR AU - Wan, Y. W. AU - Allen, G. I. AU - Liu, Z. PY - 2015 DA - 2015// TI - Tcga2stat: simple tcga data access for integrated statistical analysis in R JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btv677 DO - 10.1093/bioinformatics/btv677 ID - Wan2015 ER - TY - STD TI - cBioPortal. http://www.cbioportal.org/. Accessed 13 Feb 2017. UR - http://www.cbioportal.org/ ID - ref4 ER - TY - JOUR AU - Fernandez-Banet, J. AU - Esposito, A. AU - Coffin, S. AU - Horvath, I. B. AU - Estrella, H. AU - Schefzick, S. AU - Deng, S. AU - Wang, K. AU - AChing, K. AU - Ding, Y. PY - 2016 DA - 2016// TI - Oasis: web-based platform for exploring cancer multi-omics data JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.3692 DO - 10.1038/nmeth.3692 ID - Fernandez-Banet2016 ER - TY - JOUR AU - Zhu, J. AU - Shi, Z. AU - Wang, J. AU - Zhang, B. PY - 2014 DA - 2014// TI - Empowering biologists with multi-omics data: colorectal cancer as a paradigm JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu834 DO - 10.1093/bioinformatics/btu834 ID - Zhu2014 ER - TY - STD TI - FIREHOSE Broad GDAC. http://gdac.broadinstitute.org/. Accessed 13 Feb 2017. UR - http://gdac.broadinstitute.org/ ID - ref7 ER - TY - JOUR AU - Onitilo, A. A. AU - Engel, J. M. AU - Greenlee, R. T. AU - Mukesh, B. N. PY - 2009 DA - 2009// TI - Breast cancer subtypes based on er/pr and her2 expression: comparison of clinicopathologic features and survival JO - Clin Med Res VL - 7 UR - https://doi.org/10.3121/cmr.2008.825 DO - 10.3121/cmr.2008.825 ID - Onitilo2009 ER - TY - JOUR AU - Trichopoulos, D. AU - MacMahon, B. AU - Cole, P. PY - 1972 DA - 1972// TI - Menopause and breast cancer risk JO - J Natl Cancer Inst VL - 48 ID - Trichopoulos1972 ER - TY - JOUR AU - Vogelstein, B. AU - Papadopoulos, N. AU - Velculescu, V. E. AU - Zhou, S. AU - Diaz, L. A. AU - Kinzler, K. W. PY - 2013 DA - 2013// TI - Cancer genome landscapes JO - Science VL - 339 UR - https://doi.org/10.1126/science.1235122 DO - 10.1126/science.1235122 ID - Vogelstein2013 ER - TY - JOUR AU - Parker, J. S. AU - Mullins, M. AU - Cheang, M. C. AU - Leung, S. AU - Voduc, D. AU - Vickery, T. AU - Davies, S. AU - Fauron, C. AU - He, X. AU - Hu, Z. PY - 2009 DA - 2009// TI - Supervised risk predictor of breast cancer based on intrinsic subtypes JO - J Clin Oncol VL - 27 UR - https://doi.org/10.1200/JCO.2008.18.1370 DO - 10.1200/JCO.2008.18.1370 ID - Parker2009 ER - TY - STD TI - KEGG API. http://www.kegg.jp/kegg/docs/keggapi.html. Accessed 7 Aug 2017. UR - http://www.kegg.jp/kegg/docs/keggapi.html ID - ref12 ER - TY - STD TI - KEGG Pathway. http://www.genome.jp/kegg/pathway.html. Accessed 7 Aug 2017. UR - http://www.genome.jp/kegg/pathway.html ID - ref13 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Kawashima, S. AU - Okuno, Y. AU - Hattori, M. PY - 2004 DA - 2004// TI - The kegg resource for deciphering the genome JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh063 DO - 10.1093/nar/gkh063 ID - Kanehisa2004 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 - Bovolenta, L. A. AU - Acencio, M. L. AU - Lemke, N. PY - 2012 DA - 2012// TI - Htridb: an open-access database for experimentally verified human transcriptional regulation interactions JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-405 DO - 10.1186/1471-2164-13-405 ID - Bovolenta2012 ER - TY - JOUR AU - Liberzon, A. AU - Birger, C. AU - Thorvaldsdóttir, H. AU - Ghandi, M. AU - Mesirov, J. P. AU - Tamayo, P. PY - 2015 DA - 2015// TI - The molecular signatures database hallmark gene set collection JO - Cell Syst VL - 1 UR - https://doi.org/10.1016/j.cels.2015.12.004 DO - 10.1016/j.cels.2015.12.004 ID - Liberzon2015 ER - TY - STD TI - Cancer Gene Census. https://cancer.sanger.ac.uk/census/. Accessed 23 Aug 2017. UR - https://cancer.sanger.ac.uk/census/ ID - ref19 ER - TY - STD TI - VENN Diagram. https://github.com/benfred/venn.js/. Accessed 7 Aug 2017. UR - https://github.com/benfred/venn.js/ ID - ref20 ER - TY - JOUR AU - Leiserson, M. D. AU - Wu, H. T. AU - Vandin, F. AU - Raphael, B. J. PY - 2015 DA - 2015// TI - Comet: a statistical approach to identify combinations of mutually exclusive alterations in cancer JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0700-7 DO - 10.1186/s13059-015-0700-7 ID - Leiserson2015 ER - TY - JOUR AU - Ciriello, G. AU - Cerami, E. AU - Sander, C. AU - Schultz, N. PY - 2012 DA - 2012// TI - Mutual exclusivity analysis identifies oncogenic network modules JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.125567.111 DO - 10.1101/gr.125567.111 ID - Ciriello2012 ER - TY - STD TI - ComplexHeatmap. https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html. Accessed 13 Feb 2017. UR - https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html ID - ref23 ER - TY - JOUR AU - Fielding, R. T. AU - Taylor, R. N. PY - 2002 DA - 2002// TI - Principled design of the modern web architecture JO - ACM Trans Internet Technol (TOIT) VL - 2 UR - https://doi.org/10.1145/514183.514185 DO - 10.1145/514183.514185 ID - Fielding2002 ER -