Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gilette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS. 2005, 102 (43): 15545-50. 10.1073/pnas.0506580102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Goeman JJ, Bühlmann P: Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics. 2007
Google Scholar
Dinu I: Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics. 2007
Google Scholar
Holec M, Zelezny F, Klema J, Tolar J: Integrating Multiple-Platform Expression Data through Gene Set Features. The 5th International Symposium on Bioinformatics Research and Applications (ISBRA 2009). 2009, Springer
Google Scholar
Mootha V, Lindgren C: SL: PGC-1-alpha-responsive genes involved in oxidative phosphorylation are coorinately down regulated in human diabetes. Nature Genetics. 2003, 34: 267-273. 10.1038/ng1180.
Article
CAS
PubMed
Google Scholar
Huang DWW, Sherman BTT, Lempicki RAA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research. 2008
Google Scholar
Tomfohr J, Lu J, Kepler TB: Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics. 2005, 6: 225-10.1186/1471-2105-6-225.
Article
PubMed Central
PubMed
Google Scholar
Hastie T, Tibshirani R, Friedman J: The Elements of Statistical Learning. 2001, Springer
Book
Google Scholar
Golub TR, Slonim DK, Tamayo P, C Huard MG, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES: Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science. 1999, 286 (5439): 531-537. 10.1126/science.286.5439.531.
Article
CAS
PubMed
Google Scholar
Mitchell T: Machine Learning. 1997, McGraw Hill
Google Scholar
Vapnik VN: The Nature of Statistical Learning. 2000, Springer
Book
Google Scholar
Gamberger D, Lavrac N, Zelezny F, Tolar J: Induction of comprehensible models for gene expression datasets by subgroup discovery methodology. Journal of Biomedical Informatics. 2004, 34 (4): 269-284.
Article
Google Scholar
Zintzaras E, Kowald A: Forest classification trees and forest support vector machines algorithms: Demonstration using microarray data. Cell Cycle. 2010, 40 (5): 519-24.
Google Scholar
Huang J, Fang H, Tong W, X XF: Decision forest for classification of gene expression data. Cell Cycle. 2010,
Google Scholar
Liu J, Hughes-Oliver JM, Menius JA: Domain-enhanced analysis of microarray data using GO annotations. Bioinformatics. 2007, 23 (10): 1225-34. 10.1093/bioinformatics/btm092.
Article
CAS
PubMed
Google Scholar
Chen X, Wang L, Smith JD, Zhang B: Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics. 2008, 24 (21): 2474-81. 10.1093/bioinformatics/btn458.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guo Z, Zhang T, Li X, Wang Q, Xu J, Yu H, Zhu J, Wang H, Wang C, Topol EJ, Rao S: Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics. 2005, 6: 58+-10.1186/1471-2105-6-58.
Article
PubMed Central
PubMed
Google Scholar
Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA, Marks JR, Dressman HK, West M, Nevins JR: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2005, 439 (7074): 353-357.
Article
PubMed
Google Scholar
Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY: Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell stem cell. 2008, 2 (4): 333-344. 10.1016/j.stem.2008.02.009.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee E, Chuang HYY, Kim JWW, Ideker T, Lee D: Inferring pathway activity toward precise disease classification. PLoS computational biology. 2008, 4 (11): e1000217+-
Article
PubMed Central
PubMed
Google Scholar
Abraham G, Kowalczyk A, Loi S, Haviv I, Zobel J: Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics. 2010, 11: 277+-10.1186/1471-2105-11-277.
Article
PubMed Central
PubMed
Google Scholar
Mramor M, Toplak M, Leban G, Curk T, Demsar J, Zupan B: On utility of gene set signatures in gene expression-based cancer class prediction. JMLR Workshop and Conference Proceedings Volume 8: Machine Learning in Systems Biology. 2010, 55-64.
Google Scholar
Liu H, Motoda H: Feature Selection for Knowledge Discovery and Data Mining. 1998, Kluwer
Book
Google Scholar
Allison DB, Cui X, Page GP, Sabripour M: Microarray data analysis: from disarray to consolidation and consensus. Nature reviews. Genetics. 2006, 7: 55-65. 10.1038/nrg1749.
Article
CAS
PubMed
Google Scholar
Demšar J: Statistical Comparisons of Classifiers over Multiple Data Sets. Journal of Machine Learning Research. 2006, 7: 1-30.
Google Scholar
Guyon I, Weston J, Barnhill S, Vapnik V: Gene Selection for Cancer Classification using Support Vector Machines. mlj. 2002, 46: 389-422.
Google Scholar
Huang DW, Sherman BT, Lempick RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols. 2009, 4: 44-57.
Article
CAS
Google Scholar
Ho T: The random subspace method for constructing decision forests. Transactions on Pattern Analysis and Machine Intelligence. 1997, 20 (8): 832-44.
Google Scholar
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R: A novel signaling pathway impact analysis. Bioinformatics. 2009, 25: 77-82. 10.1093/bioinformatics/btp195.
Article
Google Scholar
Witten IH, Frank E: Data Mining: Practical machine learning tools and techniques. 2005, Morgan Kaufmann, San Francisco, 2
Google Scholar
Laiho P, Kokko A, Vanharanta S, Salovaara R, Sammalkorpi H, Järvinen H, Mecklin JP, Karttunen TJ, Tuppurainen K, Davalos V, Schwartz S, Arango D, Mäkinen MJ, Aaltonen LA: Serrated carcinomas form a subclass of colorectal cancer with distinct molecular basis. Oncogene. 2007, 26 (2): 312-20. 10.1038/sj.onc.1209778.
Article
CAS
PubMed
Google Scholar
Armstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, Minden MD, Sallan SE, Lander ES, Golub TR, Korsmeyer SJ: MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nature Genetics. 2002, 30: 41-7. 10.1038/ng765. [http://www.ncbi.nlm.nih.gov/pubmed/11731795]
Article
CAS
PubMed
Google Scholar
Farmer P, Bonnefoi H, Becette V, Tubiana-Hulin M, Fumoleau P, Larsimont D, Macgrogan G, Bergh J, Cameron D, Goldstein D, Duss S, Nicoulaz AL, Brisken C, Fiche M, Delorenzi M, Iggo R: Identification of molecular apocrine breast tumours by microarray analysis. Oncogene. 2005, 24 (29): 4660-71. 10.1038/sj.onc.1208561.
Article
CAS
PubMed
Google Scholar
Cutcliffe C, Kersey D, Huang CC, Zeng Y, Walterhouse D, Perlman EJ: Clear cell sarcoma of the kidney: up-regulation of neural markers with activation of the sonic hedgehog and Akt pathways. Clinical cancer research : an official journal of the American Association for Cancer Research. 2005, 11 (22): 7986-94. 10.1158/1078-0432.CCR-05-1354.
Article
CAS
Google Scholar
Burczynski ME, Peterson RL, Twine NC, Zuberek KA, Brodeur BJ, Casciotti L, Maganti V, Reddy PS, Strahs A, Immermann F, Spinelli W, Schwertschlag U, Slager AM, Cotreau MM, Dorner AJ: Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells. The Journal of molecular diagnostics : JMD. 2006, 8: 51-61. 10.2353/jmoldx.2006.050079.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hippo Y, Taniguchi H, Tsutsumi S, Machida N, Chong JM, Fukayama M, Kodama T, Aburatani H: Global Gene Expression Analysis of Gastric Cancer by Oligonucleotide Microarrays. Cancer Res. 2002, 62: 233-240.
CAS
PubMed
Google Scholar
Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF: Gene expression profiling of gliomas strongly predicts survival. Cancer research. 2004, 64 (18): 6503-10. 10.1158/0008-5472.CAN-04-0452.
Article
CAS
PubMed
Google Scholar
Sun L, Hui AM, Su Q, Vortmeyer A, Kotliarov Y, Pastorino S, Passaniti A, Menon J, Walling J, Bailey R, Rosenblum M, Mikkelsen T, Fine HA: Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer cell. 2006, 9 (4): 287-300. 10.1016/j.ccr.2006.03.003.
Article
CAS
PubMed
Google Scholar
Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proceedings of the National Academy of Sciences of the United States of America. 2001, 98 (24): 13790-1375. 10.1073/pnas.191502998.
Article
PubMed Central
CAS
PubMed
Google Scholar
Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med. 2002, 8 (8): 816-824.
CAS
PubMed
Google Scholar
Spira A, Beane JE, Shah V, Steiling K, Liu G, Schembri F, Gilman S, Dumas YM, Calner P, Sebastiani P, Sridhar S, Beamis J, Lamb C, Anderson T, Gerry N, Keane J, Lenburg ME, Brody JS: Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nature medicine. 2007, 13 (3): 361-6. 10.1038/nm1556.
Article
CAS
PubMed
Google Scholar
Talantov D, Mazumder A, Yu JX, Briggs T, Jiang Y, Backus J, Atkins D, Wang Y: Novel genes associated with malignant melanoma but not benign melanocytic lesions. Clinical cancer research : an official journal of the American Association for Cancer Research. 2005, 11 (20): 7234-42. 10.1158/1078-0432.CCR-05-0683.
Article
CAS
Google Scholar
Scherzer CR, Eklund AC, Morse LJ, Liao Z, Locascio JJ, Fefer D, Schwarzschild MA, Schlossmacher MG, Hauser MA, Vance JM, Sudarsky LR, Standaert DG, Growdon JH, Jensen RV, Gullans SR: Molecular markers of early Parkinson's disease based on gene expression in blood. Proceedings of the National Academy of Sciences of the United States of America. 2007, 104 (3): 955-60. 10.1073/pnas.0610204104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dahia PLM, Ross KN, Wright ME, Hayashida CY, Santagata S, Barontini M, Kung AL, Sanso G, Powers JF, Tischler AS, Hodin R, Heitritter S, Moore F, Dluhy R, Sosa JA, Ocal IT, Benn DE, Marsh DJ, Robinson BG, Schneider K, Garber J, Arum SM, Korbonits M, Grossman A, Pigny P, Toledo SPA, Nosé V, Li C, Stiles CD: A HIF1alpha regulatory loop links hypoxia and mitochondrial signals in pheochromocytomas. PLoS genetics. 2005, 1: 72-80.
Article
CAS
PubMed
Google Scholar
Gordon GJ: Transcriptional profiling of mesothelioma using microarrays. Lung cancer (Amsterdam, Netherlands). 2005, 49 (Suppl 1): S99-S103.
Article
Google Scholar
Libalova H, Dostal MPR, Topinka J, Sram RJ: Gene Expression Profiling in Blood of Asthmatic Children Living in Polluted Region of the Czech Republic (Project AIRGEN). 10th International Conference on Environmental Mutagens. 2010
Google Scholar
Best CJM, Gillespie JW, Yi Y, Chandramouli GVR, Perlmutter MA, Gathright Y, Erickson HS, Georgevich L, Tangrea MA, Duray PH, González S, Velasco A, Linehan WM, Matusik RJ, Price DK, Figg WD, Emmert-Buck MR, Chuaqui RF: Molecular alterations in primary prostate cancer after androgen ablation therapy. Clinical cancer research : an official journal of the American Association for Cancer Research. 2005, 11 (19 Pt 1): 6823-34.
Article
CAS
Google Scholar
Yoon SS, Segal NH, Park PJ, Detwiller KY, Fernando NT, Ryeom SW, Brennan MF, Singer S: Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression. The Journal of surgical research. 2006, 135 (2): 282-90. 10.1016/j.jss.2006.01.023.
Article
CAS
PubMed
Google Scholar
Carolan BJ, Heguy A, Harvey BG, Leopold PL, Ferris B, Crystal RG: Up-regulation of expression of the ubiquitin carboxyl-terminal hydrolase L1 gene in human airway epithelium of cigarette smokers. Cancer research. 2006, 66 (22): 10729-40. 10.1158/0008-5472.CAN-06-2224.
Article
CAS
PubMed
Google Scholar
Kuriakose MA, Chen WT, He ZM, Sikora AG, Zhang P, Zhang ZY, Qiu WL, Hsu DF, McMunn-Coffran C, Brown SM, Elango EM, Delacure MD, Chen FA: Selection and validation of differentially expressed genes in head and neck cancer. Cellular and molecular life sciences : CMLS. 2004, 61 (11): 1372-83. 10.1007/s00018-004-4069-0.
Article
CAS
PubMed
Google Scholar
Gashaw I, Grümmer R, Klein-Hitpass L, Dushaj O, Bergmann M, Brehm R, Grobholz R, Kliesch S, Neuvians TP, Schmid KW, von Ostau C, Winterhager E: Gene signatures of testicular seminoma with emphasis on expression of ets variant gene 4. Cellular and molecular life sciences : CMLS. 2005, 62 (19-20): 2359-68. 10.1007/s00018-005-5250-9.
Article
CAS
PubMed
Google Scholar