{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T21:26:16Z","timestamp":1769549176466,"version":"3.49.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,1,24]],"date-time":"2011-01-24T00:00:00Z","timestamp":1295827200000},"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":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-29","type":"journal-article","created":{"date-parts":[[2011,1,25]],"date-time":"2011-01-25T07:15:00Z","timestamp":1295939700000},"source":"Crossref","is-referenced-by-count":1,"title":["Investigating the effect of paralogs on microarray gene-set analysis"],"prefix":"10.1186","volume":"12","author":[{"given":"Andre J","family":"Faure","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cathal","family":"Seoighe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicola J","family":"Mulder","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,1,24]]},"reference":[{"key":"4346_CR1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25: 25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"key":"4346_CR2","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28: 27\u201330. 10.1093\/nar\/28.1.27","journal-title":"Nucleic Acids Res"},{"issue":"43","key":"4346_CR3","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. Proc Natl Acad Sci USA 2005, 102(43):15545\u201315550. 10.1073\/pnas.0506580102","journal-title":"Proc Natl Acad Sci USA"},{"key":"4346_CR4","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. Nat Rev Genet 2006, 7: 55\u201365. 10.1038\/nrg1749","journal-title":"Nat Rev Genet"},{"issue":"6","key":"4346_CR5","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1023\/B:NERE.0000023608.29741.45","volume":"29","author":"P Pavlidis","year":"2004","unstructured":"Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E: Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res 2004, 29(6):1213\u20131222. 10.1023\/B:NERE.0000023608.29741.45","journal-title":"Neurochem Res"},{"issue":"4","key":"4346_CR6","doi-asserted-by":"publisher","first-page":"R28","DOI":"10.1186\/gb-2003-4-4-r28","volume":"4","author":"BR Zeeberg","year":"2003","unstructured":"Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4(4):R28. 10.1186\/gb-2003-4-4-r28","journal-title":"Genome Biol"},{"issue":"10","key":"4346_CR7","doi-asserted-by":"publisher","first-page":"R70","DOI":"10.1186\/gb-2003-4-10-r70","volume":"4","author":"DA Hosack","year":"2003","unstructured":"Hosack DA, Dennis GJ, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4(10):R70. 10.1186\/gb-2003-4-10-r70","journal-title":"Genome Biol"},{"issue":"4","key":"4346_CR8","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1093\/bioinformatics\/btg455","volume":"20","author":"F Al-Shahrour","year":"2004","unstructured":"Al-Shahrour F, Diaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004, 20(4):578\u2013580. 10.1093\/bioinformatics\/btg455","journal-title":"Bioinformatics"},{"issue":"7","key":"4346_CR9","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1093\/bioinformatics\/bth056","volume":"20","author":"NH Shah","year":"2004","unstructured":"Shah NH, Fedoroff NV: CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology. Bioinformatics 2004, 20(7):1196\u20131197. 10.1093\/bioinformatics\/bth056","journal-title":"Bioinformatics"},{"issue":"18","key":"4346_CR10","doi-asserted-by":"publisher","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","volume":"20","author":"EI Boyle","year":"2004","unstructured":"Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G: GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20(18):3710\u20133715. 10.1093\/bioinformatics\/bth456","journal-title":"Bioinformatics"},{"issue":"9","key":"4346_CR11","doi-asserted-by":"publisher","first-page":"1464","DOI":"10.1093\/bioinformatics\/bth088","volume":"20","author":"T Beissbarth","year":"2004","unstructured":"Beissbarth T, Speed TP: GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20(9):1464\u20131465. 10.1093\/bioinformatics\/bth088","journal-title":"Bioinformatics"},{"issue":"4","key":"4346_CR12","doi-asserted-by":"publisher","first-page":"261","DOI":"10.2165\/00822942-200403040-00009","volume":"3","author":"S Zhong","year":"2004","unstructured":"Zhong S, Storch KF, Lipan O, Kao MCJ, Weitz CJ, Wong WH: GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space. Appl Bioinformatics 2004, 3(4):261\u2013264. 10.2165\/00822942-200403040-00009","journal-title":"Appl Bioinformatics"},{"issue":"9","key":"4346_CR13","doi-asserted-by":"publisher","first-page":"1462","DOI":"10.1093\/bioinformatics\/bth087","volume":"20","author":"J Cheng","year":"2004","unstructured":"Cheng J, Sun S, Tracy A, Hubbell E, Morris J, Valmeekam V, Kimbrough A, Cline MS, Liu G, Shigeta R, Kulp D, Siani-Rose MA: NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics 2004, 20(9):1462\u20131463. 10.1093\/bioinformatics\/bth087","journal-title":"Bioinformatics"},{"issue":"25","key":"4346_CR14","doi-asserted-by":"publisher","first-page":"8961","DOI":"10.1073\/pnas.0502674102","volume":"102","author":"KH Pan","year":"2005","unstructured":"Pan KH, Lih CJ, Cohen SN: Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays. Proc Natl Acad Sci USA 2005, 102(25):8961\u20138965. 10.1073\/pnas.0502674102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"4346_CR15","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","volume":"23","author":"JJ Goeman","year":"2007","unstructured":"Goeman JJ, Buhlmann P: Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007, 23(8):980\u2013987. 10.1093\/bioinformatics\/btm051","journal-title":"Bioinformatics"},{"issue":"3","key":"4346_CR16","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1038\/ng1180","volume":"34","author":"VK Mootha","year":"2003","unstructured":"Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC: PGC-lalpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003, 34(3):267\u2013273. 10.1038\/ng1180","journal-title":"Nat Genet"},{"issue":"7","key":"4346_CR17","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/ng0704-663a","volume":"36","author":"D Damian","year":"2004","unstructured":"Damian D, Gorfine M: Statistical concerns about the GSEA procedure. Nat Genet 2004, 36(7):663. author reply 663 author reply 663 10.1038\/ng0704-663a","journal-title":"Nat Genet"},{"key":"4346_CR18","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1186\/1471-2105-8-242","volume":"8","author":"I Dinu","year":"2007","unstructured":"Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y: Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics 2007, 8: 242. 10.1186\/1471-2105-8-242","journal-title":"BMC Bioinformatics"},{"key":"4346_CR19","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":"4346_CR20","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/bioinformatics\/btg382","volume":"20","author":"JJ Goeman","year":"2004","unstructured":"Goeman JJ, van de Geer SA, 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"},{"issue":"3","key":"4346_CR21","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1055\/s-0038-1633982","volume":"44","author":"U Mansmann","year":"2005","unstructured":"Mansmann U, Meister R: Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach. Methods Inf Med 2005, 44(3):449\u2013453.","journal-title":"Methods Inf Med"},{"issue":"9","key":"4346_CR22","doi-asserted-by":"publisher","first-page":"1950","DOI":"10.1093\/bioinformatics\/bti267","volume":"21","author":"JJ Goeman","year":"2005","unstructured":"Goeman JJ, Oosting J, Cleton-Jansen AM, Anninga JK, van Houwelingen HC: Testing association of a pathway with survival using gene expression data. Bioinformatics 2005, 21(9):1950\u20131957. 10.1093\/bioinformatics\/bti267","journal-title":"Bioinformatics"},{"issue":"9","key":"4346_CR23","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"VG Tusher","year":"2001","unstructured":"Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(9):5116\u20135121. 10.1073\/pnas.091062498","journal-title":"Proc Natl Acad Sci USA"},{"key":"4346_CR24","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1186\/1471-2105-8-431","volume":"8","author":"Q Liu","year":"2007","unstructured":"Liu Q, Dinu I, Adewale AJ, Potter JD, Yasui Y: Comparative evaluation of gene-set analysis methods. BMC Bioinformatics 2007, 8: 431. 10.1186\/1471-2105-8-431","journal-title":"BMC Bioinformatics"},{"issue":"16","key":"4346_CR25","doi-asserted-by":"publisher","first-page":"2028","DOI":"10.1093\/bioinformatics\/btl344","volume":"22","author":"H Pang","year":"2006","unstructured":"Pang H, Lin A, Holford M, Enerson BE, Lu B, Lawton MP, Floyd E, Zhao H: Pathway analysis using random forests classification and regression. Bioinformatics 2006, 22(16):2028\u20132036. 10.1093\/bioinformatics\/btl344","journal-title":"Bioinformatics"},{"issue":"9","key":"4346_CR26","doi-asserted-by":"publisher","first-page":"R187","DOI":"10.1186\/gb-2007-8-9-r187","volume":"8","author":"GS Eichler","year":"2007","unstructured":"Eichler GS, Reimers M, Kane D, Weinstein JN: The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data. Genome Biol 2007, 8(9):R187. 10.1186\/gb-2007-8-9-r187","journal-title":"Genome Biol"},{"key":"4346_CR27","doi-asserted-by":"crossref","first-page":"Article16","DOI":"10.2202\/1544-6115.1055","volume":"3","author":"J Rahnenfuhrer","year":"2004","unstructured":"Rahnenfuhrer J, Domingues FS, Maydt J, Lengauer T: Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol 2004, 3: Article16.","journal-title":"Stat Appl Genet Mol Biol"},{"issue":"10","key":"4346_CR28","doi-asserted-by":"publisher","first-page":"1537","DOI":"10.1101\/gr.6202607","volume":"17","author":"S Draghici","year":"2007","unstructured":"Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R: A systems biology approach for pathway level analysis. Genome Res 2007, 17(10):1537\u20131545. 10.1101\/gr.6202607","journal-title":"Genome Res"},{"issue":"7","key":"4346_CR29","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1016\/j.tig.2004.05.001","volume":"20","author":"FA Kondrashov","year":"2004","unstructured":"Kondrashov FA, Koonin EV: A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet 2004, 20(7):287\u2013290. 10.1016\/j.tig.2004.05.001","journal-title":"Trends Genet"},{"issue":"2","key":"4346_CR30","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1093\/protein\/12.2.85","volume":"12","author":"B Rost","year":"1999","unstructured":"Rost B: Twilight zone of protein sequence alignments. Protein Engineering Design and Selection 1999, 12(2):85\u201394. 10.1093\/protein\/12.2.85","journal-title":"Protein Engineering Design and Selection"},{"key":"4346_CR31","doi-asserted-by":"crossref","unstructured":"Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S: NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 2004, (32 Database):D575\u20137. 10.1093\/nar\/gkh133","DOI":"10.1093\/nar\/gkh133"},{"issue":"5594","key":"4346_CR32","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1075090","volume":"298","author":"TI Lee","year":"2002","unstructured":"Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298(5594):799\u2013804. 10.1126\/science.1075090","journal-title":"Science"},{"key":"4346_CR33","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/978-1-4684-2001-2_9","volume":"43","author":"R Karp","year":"1972","unstructured":"Karp R: Reducibility among combinatorial problems. Complexity of Computer Computations 1972, 43: 85\u2013103.","journal-title":"Complexity of Computer Computations"},{"key":"4346_CR34","first-page":"75","volume-title":"Tel-Aviv University","author":"Y Caro","year":"1979","unstructured":"Caro Y: New results on the independence number. Tel-Aviv University 1979, 75\u201379."},{"key":"4346_CR35","volume-title":"Tech. rep., Bell Laboratories Technical Memorandum 81-11217-9, Murray Hill, NJ","author":"V Wei","year":"1981","unstructured":"Wei V: A lower bound on the stability number of a simple graph. Tech. rep., Bell Laboratories Technical Memorandum 81\u201311217\u20139, Murray Hill, NJ 1981."},{"issue":"2-3","key":"4346_CR36","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/S0166-218X(02)00205-6","volume":"126","author":"S Sakai","year":"2003","unstructured":"Sakai S, Togasaki M, Yamazaki K: A note on greedy algorithms for the maximum weighted independent set problem. Discrete Applied Mathematics 2003, 126(2\u20133):313\u2013322. 10.1016\/S0166-218X(02)00205-6","journal-title":"Discrete Applied Mathematics"},{"key":"4346_CR37","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/BF02523693","volume":"18","author":"M Halldorsson","year":"1997","unstructured":"Halldorsson M, Radhakrishnan J: Greed is good: approximating independent sets in sparse and bounded-degree graphs. Algorithmica 1997, 18: 145\u2013163. 10.1007\/BF02523693","journal-title":"Algorithmica"},{"issue":"5633","key":"4346_CR38","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1126\/science.1086391","volume":"301","author":"JM Alonso","year":"2003","unstructured":"Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR: Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 2003, 301(5633):653\u2013657. 10.1126\/science.1086391","journal-title":"Science"},{"key":"4346_CR39","volume-title":"Online","author":"Google Inc","year":"2010","unstructured":"Google Inc: Google Scholar. Online 2010. [ http:\/\/scholar.google.com ]"},{"issue":"27","key":"4346_CR40","doi-asserted-by":"publisher","first-page":"10143","DOI":"10.1073\/pnas.0401422101","volume":"101","author":"A Spira","year":"2004","unstructured":"Spira A, Beane J, Shah V, Liu G, Schembri F, Yang X, Palma J, Brody JS: Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci USA 2004, 101(27):10143\u201310148. 10.1073\/pnas.0401422101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"4346_CR41","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1016\/S0022-2275(20)33383-6","volume":"40","author":"A Babiker","year":"1999","unstructured":"Babiker A, Andersson O, Lindblom D, van der Linden J, Wiklund B, Lutjohann D, Diczfalusy U, Bjorkhem I: Elimination of cholesterol as cholestenoic acid in human lung by sterol 27-hydroxylase: evidence that most of this steroid in the circulation is of pulmonary origin. J Lipid Res 1999, 40(8):1417\u20131425.","journal-title":"J Lipid Res"},{"key":"4346_CR42","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/0021-9150(78)90149-1","volume":"30","author":"RJ Garrison","year":"1978","unstructured":"Garrison RJ, Kannel WB, Feinleib M, Castelli WP, McNamara PM, Padgett SJ: Cigarette smoking and HDL cholesterol: the Framingham offspring study. Atherosclerosis 1978, 30: 17\u201325. 10.1016\/0021-9150(78)90149-1","journal-title":"Atherosclerosis"},{"issue":"8947","key":"4346_CR43","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1016\/S0140-6736(95)90409-3","volume":"345","author":"ID Pavord","year":"1995","unstructured":"Pavord ID, Tattersfield AE: Bronchoprotective role for endogenous prostaglandin E2. Lancet 1995, 345(8947):436\u2013438. 10.1016\/S0140-6736(95)90409-3","journal-title":"Lancet"},{"issue":"2","key":"4346_CR44","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/S0169-5002(02)00039-9","volume":"37","author":"S Mollerup","year":"2002","unstructured":"Mollerup S, Jorgensen K, Berge G, Haugen A: Expression of estrogen receptors alpha and beta in human lung tissue and cell lines. Lung Cancer 2002, 37(2):153\u2013159. 10.1016\/S0169-5002(02)00039-9","journal-title":"Lung Cancer"},{"issue":"6","key":"4346_CR45","doi-asserted-by":"publisher","first-page":"L1154","DOI":"10.1152\/ajplung.00228.2004","volume":"287","author":"D Massaro","year":"2004","unstructured":"Massaro D, Massaro GD: Estrogen regulates pulmonary alveolar formation, loss, and regeneration in mice. Am J Physiol Lung Cell Mol Physiol 2004, 287(6):L1154\u20139. 10.1152\/ajplung.00228.2004","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"issue":"3","key":"4346_CR46","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. Brief Bioinform 2008, 9(3):189\u2013197. 10.1093\/bib\/bbn001","journal-title":"Brief Bioinform"},{"issue":"7","key":"4346_CR47","doi-asserted-by":"publisher","first-page":"2581","DOI":"10.1182\/blood-2003-04-1227","volume":"102","author":"PA Croonquist","year":"2003","unstructured":"Croonquist PA, Linden MA, Zhao F, Van Ness BG: Gene profiling of a myeloma cell line reveals similarities and unique signatures among IL-6 response, N-ras-activating mutations, and coculture with bone marrow stromal cells. Blood 2003, 102(7):2581\u20132592. 10.1182\/blood-2003-04-1227","journal-title":"Blood"},{"issue":"3","key":"4346_CR48","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/ng1518","volume":"37","author":"EJ Chesler","year":"2005","unstructured":"Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin NE, Langston MA, Threadgill DW, Manly KF, Williams RW: Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 2005, 37(3):233\u2013242. 10.1038\/ng1518","journal-title":"Nat Genet"},{"issue":"8","key":"4346_CR49","doi-asserted-by":"publisher","first-page":"2956","DOI":"10.1182\/blood-2003-09-3314","volume":"103","author":"B Bhattacharya","year":"2004","unstructured":"Bhattacharya B, Miura T, Brandenberger R, Mejido J, Luo Y, Yang AX, Joshi BH, Ginis I, Thies RS, Amit M, Lyons I, Condie BG, Itskovitz-Eldor J, Rao MS, Puri RK: Gene expression in human embryonic stem cell lines: unique molecular signature. Blood 2004, 103(8):2956\u20132964. 10.1182\/blood-2003-09-3314","journal-title":"Blood"},{"issue":"9","key":"4346_CR50","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/sj.leu.2401482","volume":"13","author":"K Tanaka","year":"1999","unstructured":"Tanaka K, Arif M, Eguchi M, Guo SX, Hayashi Y, Asaoku H, Kyo T, Dohy H, Kamada N: Frequent allelic loss of the RB, D13S319 and D13S25 locus in myeloid malignancies with deletion\/translocation at 13q14 of chromosome 13, but not in lymphoid malignancies. Leukemia 1999, 13(9):1367\u20131373. 10.1038\/sj.leu.2401482","journal-title":"Leukemia"},{"key":"4346_CR51","volume-title":"Molecular Cell Biology","author":"H Lodish","year":"2001","unstructured":"Lodish H, Berk A, Zipursky SL: In Molecular Cell Biology. Edited by: Freeman WH. 2001."},{"issue":"3","key":"4346_CR52","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1002\/(SICI)1098-2264(199607)16:3<170::AID-GCC3>3.0.CO;2-W","volume":"16","author":"EM Berns","year":"1996","unstructured":"Berns EM, Klijn JG, Smid M, van Staveren IL, Look MP, van Putten WL, Foekens JA: TP53 and MYC gene alterations independently predict poor prognosis in breast cancer patients. Genes Chromosomes Cancer 1996, 16(3):170\u2013179. 10.1002\/(SICI)1098-2264(199607)16:3<170::AID-GCC3>3.0.CO;2-W","journal-title":"Genes Chromosomes Cancer"},{"issue":"8","key":"4346_CR53","first-page":"2425","volume":"7","author":"MA Grotzer","year":"2001","unstructured":"Grotzer MA, Hogarty MD, Janss AJ, Liu X, Zhao H, Eggert A, Sutton LN, Rorke LB, Brodeur GM, Phillips PC: MYC messenger RNA expression predicts survival outcome in childhood primitive neuroectodermal tumor\/medulloblastoma. Clin Cancer Res 2001, 7(8):2425\u20132433.","journal-title":"Clin Cancer Res"},{"issue":"3","key":"4346_CR54","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1172\/JCI6863","volume":"104","author":"F Bunz","year":"1999","unstructured":"Bunz F, Hwang PM, Torrance C, Waldman T, Zhang Y, Dillehay L, Williams J, Lengauer C, Kinzler KW, Vogelstein B: Disruption of p53 in human cancer cells alters the responses to therapeutic agents. J Clin Invest 1999, 104(3):263\u2013269. 10.1172\/JCI6863","journal-title":"J Clin Invest"},{"key":"4346_CR55","doi-asserted-by":"crossref","unstructured":"UniProt: The universal protein resource (UniProt). Nucleic Acids Res 2008, (36 Database):D190\u20135.","DOI":"10.1093\/nar\/gkm895"},{"issue":"6","key":"4346_CR56","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"},{"issue":"468","key":"4346_CR57","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1198\/016214504000000683","volume":"99","author":"Z Wu","year":"2004","unstructured":"Wu Z, Irizarry R, Gentleman R, Martinez-Murillo F, Spencer F: A Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal ofthe American Statistical Association 2004, 99(468):909\u2013918. 10.1198\/016214504000000683","journal-title":"Journal ofthe American Statistical Association"},{"key":"4346_CR58","volume-title":"Online","author":"W Moreira","year":"2010","unstructured":"Moreira W, Warnes GR, Gautier L: RPy home page. Online 2010. [ http:\/\/rpy.sourceforge.net\/ ]"},{"key":"4346_CR59","volume-title":"Online","author":"R Foundation","year":"2010","unstructured":"R Foundation: The R Project for Statistical Computing. Online 2010. [ http:\/\/www.r-project.org\/ ]"},{"key":"4346_CR60","volume-title":"Online","author":"WebPy","year":"2008","unstructured":"WebPy: Web.py: Think about the ideal way to write a web app. write the code to make it happen. Online 2008. [ http:\/\/webpy.org ]"},{"issue":"13","key":"4346_CR61","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","volume":"22","author":"A Alexa","year":"2006","unstructured":"Alexa A, Rahnenfuhrer J, Lengauer T: Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006, 22(13):1600\u20131607. 10.1093\/bioinformatics\/btl140","journal-title":"Bioinformatics"},{"key":"4346_CR62","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/1471-2105-6-168","volume":"6","author":"BR Zeeberg","year":"2005","unstructured":"Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN: High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 2005, 6: 168. 10.1186\/1471-2105-6-168","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"4346_CR63","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1002\/humu.10081","volume":"19","author":"M Olivier","year":"2002","unstructured":"Olivier M, Eeles R, Hollstein M, Khan MA, Harris CC, Hainaut P: The IARC TP53 database: new online mutation analysis and recommendations to users. Hum Mutat 2002, 19(6):607\u2013614. 10.1002\/humu.10081","journal-title":"Hum Mutat"},{"key":"4346_CR64","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/ng765","volume":"30","author":"SA Armstrong","year":"2002","unstructured":"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. Nat Genet 2002, 30: 41\u201347. 10.1038\/ng765","journal-title":"Nat Genet"},{"issue":"24","key":"4346_CR65","doi-asserted-by":"publisher","first-page":"13790","DOI":"10.1073\/pnas.191502998","volume":"98","author":"A Bhattacharjee","year":"2001","unstructured":"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. Proc Natl Acad Sci USA 2001, 98(24):13790\u201313795. 10.1073\/pnas.191502998","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"4346_CR66","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1038\/nm733","volume":"8","author":"DG Beer","year":"2002","unstructured":"Beer DG, Kardia SLR, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JMG, Iannettoni MD, Orringer MB, Hanash S: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 8(8):816\u2013824.","journal-title":"Nat Med"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-29.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-29\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-29.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T01:29:15Z","timestamp":1637198955000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-29"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,1,24]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4346"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-29","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,1,24]]},"article-number":"29"}}