{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T09:45:00Z","timestamp":1774950300286,"version":"3.50.1"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,1,1]],"date-time":"2010-01-01T00:00:00Z","timestamp":1262304000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1471-2105-11-1","type":"journal-article","created":{"date-parts":[[2010,1,1]],"date-time":"2010-01-01T02:14:26Z","timestamp":1262312066000},"source":"Crossref","is-referenced-by-count":645,"title":["Detection of gene pathways with predictive power for breast cancer prognosis"],"prefix":"10.1186","volume":"11","author":[{"given":"Shuangge","family":"Ma","sequence":"first","affiliation":[]},{"given":"Michael R","family":"Kosorok","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,1,1]]},"reference":[{"key":"3458_CR1","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1146\/annurev.pathmechdis.3.121806.151505","volume":"3","author":"M Cheang","year":"2008","unstructured":"Cheang M, Rijn M, Nielsen TO: Gene expression profiling of breast cancer. Annual Review of Pathology: Mechanisms of Disease 2008, 3: 67\u201397. 10.1146\/annurev.pathmechdis.3.121806.151505","journal-title":"Annual Review of Pathology: Mechanisms of Disease"},{"key":"3458_CR2","doi-asserted-by":"publisher","DOI":"10.1002\/0470041102","volume-title":"Cancer Diagnostics with DNA Microarrays","author":"S Knudsen","year":"2006","unstructured":"Knudsen S: Cancer Diagnostics with DNA Microarrays. Liss: Wiley; 2006."},{"key":"3458_CR3","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1093\/jnci\/djj052","volume":"98","author":"C Sotiriou","year":"2006","unstructured":"Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, Vijver MJ, Bergh J, Piccart M, Delorenzi M: Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. JNCI 2006, 98: 262\u2013272.","journal-title":"JNCI"},{"key":"3458_CR4","doi-asserted-by":"publisher","first-page":"10292","DOI":"10.1158\/0008-5472.CAN-05-4414","volume":"66","author":"AV Ivshina","year":"2006","unstructured":"Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, Wong JE, Liu ET, Bergh J, Kuznetsov VA, Miller LD: Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Research 2006, 66: 10292\u201310301. 10.1158\/0008-5472.CAN-05-4414","journal-title":"Cancer Research"},{"key":"3458_CR5","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1038\/415530a","volume":"415","author":"LJ van't Veer","year":"2002","unstructured":"van't Veer LJ, Dai H, Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415: 530\u2013536. 10.1038\/415530a","journal-title":"Nature"},{"key":"3458_CR6","doi-asserted-by":"publisher","first-page":"1999","DOI":"10.1056\/NEJMoa021967","volume":"347","author":"MJvan de Vijver","year":"2002","unstructured":"Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene expression signature as a predictor of survival in breast cancer. NEJM 2002, 347: 1999\u20132009. 10.1056\/NEJMoa021967","journal-title":"NEJM"},{"key":"3458_CR7","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1016\/j.tibtech.2005.05.011","volume":"23","author":"RK Curtis","year":"2005","unstructured":"Curtis RK, Oresic M, Vidal-Puiq A: Pathways to the analysis of microarray data. Trends in Biotechnology 2005, 23: 429\u2013435. 10.1016\/j.tibtech.2005.05.011","journal-title":"Trends in Biotechnology"},{"key":"3458_CR8","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette 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: 15545\u201315550. 10.1073\/pnas.0506580102","journal-title":"PNAS"},{"key":"3458_CR9","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/bioinformatics\/btg382","volume":"20","author":"JJ Goeman","year":"2004","unstructured":"Goeman JJ, Geer S, de Kort F, van Houwelingen HC: A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20: 93\u201399. 10.1093\/bioinformatics\/btg382","journal-title":"Bioinformatics"},{"key":"3458_CR10","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1214\/07-AOAS101","volume":"1","author":"B Efron","year":"2007","unstructured":"Efron B, Tibshirani R: On testing the significance of sets of genes. Annals of Applied Statistics 2007, 1: 107\u2013129. 10.1214\/07-AOAS101","journal-title":"Annals of Applied Statistics"},{"key":"3458_CR11","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nrg1749","volume":"7","author":"DB Allison","year":"2006","unstructured":"Allison DB, Cui X, Page GP, Sabripour M: Microarray data analysis: from disarray to consolidation and consensus. Nature Reviews Genetics 2006, 7: 55\u201365. 10.1038\/nrg1749","journal-title":"Nature Reviews Genetics"},{"key":"3458_CR12","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/1471-2105-10-47","volume":"10","author":"M Ackermann","year":"2009","unstructured":"Ackermann M, Strimmer K: A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 10: 47. 10.1186\/1471-2105-10-47","journal-title":"BMC Bioinformatics"},{"key":"3458_CR13","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1093\/bib\/bbn001","volume":"9","author":"D Nam","year":"2008","unstructured":"Nam D, Kim SY: Gene-set approach for expression pattern analysis. Briefings in Bioinformatics 2008, 9: 189\u2013197. 10.1093\/bib\/bbn001","journal-title":"Briefings in Bioinformatics"},{"key":"3458_CR14","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1093\/jnci\/95.1.14","volume":"95","author":"R Simon","year":"2003","unstructured":"Simon R, Radmacher MD, Dobbin K, McShane LM: Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. JNCI 2003, 95: 14\u201318.","journal-title":"JNCI"},{"key":"3458_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-10-1","volume":"10","author":"S Ma","year":"2009","unstructured":"Ma S, Huang J: Regularized gene selection in cancer microarray meta-analysis. BMC Bioinformatics 2009, 10: 1. 10.1186\/1471-2105-10-1","journal-title":"BMC Bioinformatics"},{"key":"3458_CR16","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/1471-2164-5-94","volume":"5","author":"R Shen","year":"2004","unstructured":"Shen R, Ghosh D, Chinnaiyan A: Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. BMC Genomics 2004, 5: 94. 10.1186\/1471-2164-5-94","journal-title":"BMC Genomics"},{"key":"3458_CR17","doi-asserted-by":"publisher","first-page":"10393","DOI":"10.1073\/pnas.1732912100","volume":"100","author":"C Sotiriou","year":"2003","unstructured":"Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET: Breast cancer classification and prognosis based on gene expression profiles from a population based study. PNAS 2003, 100: 10393\u201310398. 10.1073\/pnas.1732912100","journal-title":"PNAS"},{"key":"3458_CR18","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.jss.2005.11.012","volume":"130","author":"D Gorski","year":"2006","unstructured":"Gorski D, Schell SR, Kounalakis N, Torres K, Barnard NJ, Goydos JS, Chen S: Elevated metabotropic glutamate receptor expression: A novel finding in invasive breast cancer. Journal of Surgical Research 2006, 130: 164\u2013164. 10.1016\/j.jss.2005.11.012","journal-title":"Journal of Surgical Research"},{"key":"3458_CR19","unstructured":"Comparative Toxigenomics Database[\n                    http:\/\/ctd.mdibl.org\/\n                    \n                  ]"},{"key":"3458_CR20","unstructured":"US Patent 75142090[\n                    http:\/\/www.faqs.org\/patents\/app\/20090157326\n                    \n                  ]"},{"key":"3458_CR21","first-page":"5979","volume":"61","author":"S Gruvberger","year":"2001","unstructured":"Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, Ferno M, Peterson C, Meltzer PS: Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Research 2001, 61: 5979\u20135984.","journal-title":"Cancer Research"},{"key":"3458_CR22","doi-asserted-by":"publisher","first-page":"2261","DOI":"10.1200\/JCO.2005.03.8802","volume":"24","author":"M Smid","year":"2006","unstructured":"Smid M, Wang Y, Klijn JG, Sieuwerts AM, Zhang Y, Atkins D, Martens JW, Foekens JA: Genes associated with breast cancer metastatic to bone. Journal of Clinical Oncology 2006, 24: 2261\u20132267. 10.1200\/JCO.2005.03.8802","journal-title":"Journal of Clinical Oncology"},{"key":"3458_CR23","unstructured":"Genes-to-Systems Breast Cancer Database[\n                    http:\/\/www.itb.cnr.it\/breastcancer\/php\/nodeVisitors.php?idGO=GO:0046872\n                    \n                  ]"},{"key":"3458_CR24","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1074\/mcp.M800493-MCP200","volume":"8","author":"A Umar","year":"2009","unstructured":"Umar A, Kang H, Timmermans AM, Look MP, Meijer-van Gelder ME, den Bakker MA, Jaitly N, Martens JWM, Luider TM, Foekens JA, Pasa-Tolic L: Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer. Molecular & Cellular Proteomics 2009, 8: 1278\u20131294. 10.1074\/mcp.M800493-MCP200","journal-title":"Molecular & Cellular Proteomics"},{"key":"3458_CR25","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1023\/A:1020950420196","volume":"19","author":"SY Yang","year":"2002","unstructured":"Yang SY, Lee J, Park CG, Kim S, Hong S, Chung HC, Min SK, Han JW, Lee HW, Lee HY: Expression of autotaxin (NPP-2) is closely linked to invasiveness of breast cancer cells. Clinical & Experimental Metastasis 2002, 19: 603\u2013608. 10.1023\/A:1020950420196","journal-title":"Clinical & Experimental Metastasis"},{"key":"3458_CR26","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/j.ccr.2009.03.027","volume":"15","author":"S Liu","year":"2009","unstructured":"Liu S, Umezu-Goto M, Murph M, Lu Y, Liu W, Zhang F, Yu S, Stephens LC, Cui X, Murrow G, Coombes K, Muller W, Hung MC, Perou CM, Lee AV, Fang X, Mills GB: Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases. Cancer Cell 2009, 15: 539\u2013550. 10.1016\/j.ccr.2009.03.027","journal-title":"Cancer Cell"},{"key":"3458_CR27","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1007\/s00432-007-0318-6","volume":"134","author":"M Tomida","year":"2008","unstructured":"Tomida M, Ohtake H, Yokota T, Kobayashi Y, Kurosumi M: Stat3 up-regulates expression of nicotinamide N-methyltransferase in human cancer cells. Journal of Cancer Research and Clinical Oncology 2008, 134: 551\u2013559. 10.1007\/s00432-007-0318-6","journal-title":"Journal of Cancer Research and Clinical Oncology"},{"key":"3458_CR28","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1002\/path.2385","volume":"216","author":"NS Nguyen Huu","year":"2008","unstructured":"Nguyen Huu NS, Ryder WD, Zeps N, Flasza M, Chiu M, Hanby AM, Poulsom R, Clarke RB, Baron M: Tumour-promoting activity of altered WWP1 expression in breast cancer and its utility as a prognostic indicator. Journal of Pathology 2008, 216: 93\u2013102. 10.1002\/path.2385","journal-title":"Journal of Pathology"},{"key":"3458_CR29","first-page":"1321","volume":"21","author":"S Blazquez","year":"2006","unstructured":"Blazquez S, Sirvent JJ, Olona M, Aguilar C, Pelegri A, Garcia JF, Palacios J: Caspase-3 and caspase-6 in ductal breast carcinoma: a descriptive study. Histology and Histopathology 2006, 21: 1321\u20131329.","journal-title":"Histology and Histopathology"},{"key":"3458_CR30","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/s10549-006-9471-x","volume":"106","author":"AM Mulligan","year":"2007","unstructured":"Mulligan AM, O'Malley FP, Ennis M, Fantus IG, Goodwin PJ: Insulin receptor is an independent predictor of a favorable outcome in early stage breast cancer. Breast Cancer Research and Treatment 2007, 106: 39\u201347. 10.1007\/s10549-006-9471-x","journal-title":"Breast Cancer Research and Treatment"},{"key":"3458_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4310\/SII.2009.v2.n1.a1","volume":"2","author":"S Ma","year":"2009","unstructured":"Ma S, Huang J, Shen S: Identification of cancer-associated gene clusters and genes via clustering penalization. Statistics and Its Interface 2009, 2: 1\u201311.","journal-title":"Statistics and Its Interface"},{"key":"3458_CR32","unstructured":"Study Website[\n                    http:\/\/publichealth.yale.edu\/faculty\/labs\/ma\/Geneset\/main.html\n                    \n                  ]"},{"key":"3458_CR33","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1093\/bioinformatics\/btp038","volume":"25","author":"DM Rocke","year":"2009","unstructured":"Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J: Papers on normalization, variable selection, classification or clustering of microarray data. Bioinformatics 2009, 25: 701\u2013702. 10.1093\/bioinformatics\/btp038","journal-title":"Bioinformatics"},{"key":"3458_CR34","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1093\/bioinformatics\/btp085","volume":"25","author":"S Ma","year":"2009","unstructured":"Ma S, Kosorok MR: Identification of differential gene pathways with principal component analysis. Bioinformatics 2009, 25: 882\u2013889. 10.1093\/bioinformatics\/btp085","journal-title":"Bioinformatics"},{"key":"3458_CR35","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1093\/bib\/bbn027","volume":"9","author":"S Ma","year":"2008","unstructured":"Ma S, Huang J: Penalized feature selection and classification in bioinformatics. Briefings in Bioinformatics 2008, 9: 392\u2013403. 10.1093\/bib\/bbn027","journal-title":"Briefings in Bioinformatics"},{"key":"3458_CR36","doi-asserted-by":"publisher","first-page":"1356","DOI":"10.1214\/aos\/1015957397","volume":"28","author":"K Knight","year":"2000","unstructured":"Knight K, Fu WJ: Asymptotics for lasso-type estimators. Annals of Statistics 2000, 28: 1356\u20131378. 10.1214\/aos\/1015957397","journal-title":"Annals of Statistics"},{"key":"3458_CR37","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1214\/009053607000000875","volume":"36","author":"J Huang","year":"2008","unstructured":"Huang J, Horowitz JL, Ma S: Asymptotic properties of bridge estimators in sparse high-dimensional regression model. Annals of Statistics 2008, 36: 587\u2013613. 10.1214\/009053607000000875","journal-title":"Annals of Statistics"},{"key":"3458_CR38","first-page":"1533","volume":"17","author":"J Huang","year":"2007","unstructured":"Huang J, Ma S, Xie H: Least absolute deviations estimation for the accelerated failure time model. Statistica Sinica 2007, 17: 1533\u20131548.","journal-title":"Statistica Sinica"},{"key":"3458_CR39","volume-title":"Counting Processes and Survival Analysis","author":"TR Fleming","year":"1991","unstructured":"Fleming TR, Harrington DP: Counting Processes and Survival Analysis. New York: Wiley; 1991."},{"key":"3458_CR40","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1214\/aos\/1176347747","volume":"18","author":"MP Jones","year":"1990","unstructured":"Jones MP, Crowley J: Asymptotic properties of a general class of nonparametric tests for survival analysis. Annals of Statistics 1990, 18: 1203\u20131220. 10.1214\/aos\/1176347747","journal-title":"Annals of Statistics"},{"key":"3458_CR41","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1080\/01621459.1999.10473847","volume":"94","author":"MR Kosorok","year":"1999","unstructured":"Kosorok MR, Lin CY: The versatility of function-indexed weighted log-rank statistics. JASA 1999, 94: 320\u2013332.","journal-title":"JASA"},{"key":"3458_CR42","volume-title":"Meta-Analysis, Decision Analysis, and Cost-Effectiveness Analysis: Methods for Quantitative Synthesis in Medicines","author":"DB Petitti","year":"2000","unstructured":"Petitti DB: Meta-Analysis, Decision Analysis, and Cost-Effectiveness Analysis: Methods for Quantitative Synthesis in Medicines. USA: Oxford University Press; 2000."},{"key":"3458_CR43","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1214\/aos\/1013699998","volume":"29","author":"Y Benjamini","year":"2001","unstructured":"Benjamini Y, Yekutieli D: The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 2001, 29: 1165\u20131188. 10.1214\/aos\/1013699998","journal-title":"Annals of Statistics"},{"key":"3458_CR44","volume-title":"Survival Analysis","author":"JP Klein","year":"2005","unstructured":"Klein JP, Moeschberger ML: Survival Analysis. Liss: Srpinger; 2005."},{"key":"3458_CR45","first-page":"2541","volume":"7","author":"P Zhao","year":"2007","unstructured":"Zhao P, Yu B: On model selection consistency of Lasso. Journal of Machine Learning Research 2007, 7: 2541\u20132567.","journal-title":"Journal of Machine Learning Research"},{"key":"3458_CR46","doi-asserted-by":"publisher","first-page":"1456","DOI":"10.1214\/009053606000001433","volume":"35","author":"MR Kosorok","year":"2007","unstructured":"Kosorok MR, Ma S: Marginal asymptotics for the \"large p, small n\" paradigm: with applications to microarray data. Annals of Statistics 2007, 35: 1456\u20131486. 10.1214\/009053606000001433","journal-title":"Annals of Statistics"},{"key":"3458_CR47","doi-asserted-by":"publisher","first-page":"10869","DOI":"10.1073\/pnas.191367098","volume":"98","author":"T Sorlie","year":"2001","unstructured":"Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lonning P, Borresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. PNAS 2001, 98: 10869\u201310874. 10.1073\/pnas.191367098","journal-title":"PNAS"},{"key":"3458_CR48","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1016\/S0140-6736(03)13308-9","volume":"361","author":"E Huang","year":"2003","unstructured":"Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT: Gene expression predictors of breast cancer outcomes. Lancet 2003, 361: 1590\u20131596. 10.1016\/S0140-6736(03)13308-9","journal-title":"Lancet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T07:38:10Z","timestamp":1548142690000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1,1]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3458"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1,1]]},"article-number":"1"}}