{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T17:26:12Z","timestamp":1780766772985,"version":"3.54.1"},"reference-count":53,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over individual gene analyses, including greater robustness, sensitivity and biological relevance. However, previous GSA methods have limited usage as they cannot handle datasets of different sample sizes or experimental designs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To address these limitations, we present a new GSA method called Generally Applicable Gene-set Enrichment (GAGE). We successfully apply GAGE to multiple microarray datasets with different sample sizes, experimental designs and profiling techniques. GAGE shows significantly better results when compared to two other commonly used GSA methods of GSEA and PAGE. We demonstrate this improvement in the following three aspects: (1) consistency across repeated studies\/experiments; (2) sensitivity and specificity; (3) biological relevance of the regulatory mechanisms inferred.<\/jats:p><jats:p>GAGE reveals novel and relevant regulatory mechanisms from both published and previously unpublished microarray studies. From two published lung cancer data sets, GAGE derived a more cohesive and predictive mechanistic scheme underlying lung cancer progress and metastasis. For a previously unpublished BMP6 study, GAGE predicted novel regulatory mechanisms for BMP6 induced osteoblast differentiation, including the canonical BMP-TGF beta signaling, JAK-STAT signaling, Wnt signaling, and estrogen signaling pathways\u2013all of which are supported by the experimental literature.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>GAGE is generally applicable to gene expression datasets with different sample sizes and experimental designs. GAGE consistently outperformed two most frequently used GSA methods and inferred statistically and biologically more relevant regulatory pathways. The GAGE method is implemented in R in the \"gage\" package, available under the GNU GPL from<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/sysbio.engin.umich.edu\/~luow\/downloads.php\" ext-link-type=\"uri\">http:\/\/sysbio.engin.umich.edu\/~luow\/downloads.php<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-10-161","type":"journal-article","created":{"date-parts":[[2009,5,27]],"date-time":"2009-05-27T18:15:53Z","timestamp":1243448153000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1200,"title":["GAGE: generally applicable gene set enrichment for pathway analysis"],"prefix":"10.1186","volume":"10","author":[{"given":"Weijun","family":"Luo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael S","family":"Friedman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerby","family":"Shedden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kurt D","family":"Hankenson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J","family":"Woolf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2009,5,27]]},"reference":[{"key":"2891_CR1","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1186\/1471-2105-9-467","volume":"9","author":"W Luo","year":"2008","unstructured":"Luo W, Hankenson KD, Woolf PJ: Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics 2008, 9: 467. 10.1186\/1471-2105-9-467","journal-title":"BMC Bioinformatics"},{"key":"2891_CR2","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: 189\u201397. 10.1093\/bib\/bbn001","journal-title":"Brief Bioinform"},{"key":"2891_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, et al.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102: 15545\u201350. 10.1073\/pnas.0506580102","journal-title":"Proc Natl Acad Sci USA"},{"key":"2891_CR4","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, et al.: PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003, 34: 267\u201373. 10.1038\/ng1180","journal-title":"Nat Genet"},{"key":"2891_CR5","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1186\/1471-2105-6-144","volume":"6","author":"SY Kim","year":"2005","unstructured":"Kim SY, Volsky DJ: PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005, 6: 144. 10.1186\/1471-2105-6-144","journal-title":"BMC Bioinformatics"},{"key":"2891_CR6","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1214\/07-AOAS104","volume":"1","author":"MA Newton","year":"2007","unstructured":"Newton MA, Quintana FA, Den Boon JA, Sengupta S, Ahlquist P: Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. Ann Appl Stat 2007, 1: 85\u2013106. 10.1214\/07-AOAS104","journal-title":"Ann Appl Stat"},{"key":"2891_CR7","doi-asserted-by":"publisher","first-page":"W592","DOI":"10.1093\/nar\/gki484","volume":"33","author":"A Boorsma","year":"2005","unstructured":"Boorsma A, Foat BC, Vis D, Klis F, Bussemaker HJ: T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res 2005, 33: W592\u20135. 10.1093\/nar\/gki484","journal-title":"Nucleic Acids Res"},{"key":"2891_CR8","doi-asserted-by":"publisher","first-page":"13544","DOI":"10.1073\/pnas.0506577102","volume":"102","author":"L Tian","year":"2005","unstructured":"Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ: Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA 2005, 102: 13544\u20139. 10.1073\/pnas.0506577102","journal-title":"Proc Natl Acad Sci USA"},{"key":"2891_CR9","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":"2891_CR10","doi-asserted-by":"publisher","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","volume":"21","author":"WT Barry","year":"2005","unstructured":"Barry WT, Nobel AB, Wright FA: Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 2005, 21: 1943\u20139. 10.1093\/bioinformatics\/bti260","journal-title":"Bioinformatics"},{"key":"2891_CR11","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: 980\u20137. 10.1093\/bioinformatics\/btm051","journal-title":"Bioinformatics"},{"key":"2891_CR12","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"},{"key":"2891_CR13","doi-asserted-by":"publisher","first-page":"W741","DOI":"10.1093\/nar\/gki475","volume":"33","author":"B Zhang","year":"2005","unstructured":"Zhang B, Kirov S, Snoddy J: WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 2005, 33: W741\u20138. 10.1093\/nar\/gki475","journal-title":"Nucleic Acids Res"},{"key":"2891_CR14","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/1471-2105-8-114","volume":"8","author":"F Al-Shahrour","year":"2007","unstructured":"Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Minguez P, Montaner D, Dopazo J: From genes to functional classes in the study of biological systems. BMC Bioinformatics 2007, 8: 114. 10.1186\/1471-2105-8-114","journal-title":"BMC Bioinformatics"},{"key":"2891_CR15","volume-title":"Brief Bioinform","author":"D Nam","year":"2008","unstructured":"Nam D, Kim SY: Gene-set approach for expression pattern analysis. Brief Bioinform 2008."},{"issue":"Suppl 6","key":"2891_CR16","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1471-2105-8-S6-S6","volume":"8","author":"HJ Bussemaker","year":"2007","unstructured":"Bussemaker HJ, Ward LD, Boorsma A: Dissecting complex transcriptional responses using pathway-level scores based on prior information. BMC Bioinformatics 2007, 8(Suppl 6):S6. 10.1186\/1471-2105-8-S6-S6","journal-title":"BMC Bioinformatics"},{"key":"2891_CR17","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/nature05354","volume":"444","author":"JA Baur","year":"2006","unstructured":"Baur JA, Pearson KJ, Price NL, Jamieson HA, Lerin C, Kalra A, Prabhu VV, Allard JS, Lopez-Lluch G, Lewis K, et al.: Resveratrol improves health and survival of mice on a high-calorie diet. Nature 2006, 444: 337\u201342. 10.1038\/nature05354","journal-title":"Nature"},{"key":"2891_CR18","doi-asserted-by":"publisher","first-page":"2618","DOI":"10.1093\/bioinformatics\/bth293","volume":"20","author":"M Smid","year":"2004","unstructured":"Smid M, Dorssers LC: GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics 2004, 20: 2618\u201325. 10.1093\/bioinformatics\/bth293","journal-title":"Bioinformatics"},{"key":"2891_CR19","doi-asserted-by":"publisher","first-page":"e151","DOI":"10.1093\/nar\/gkl766","volume":"34","author":"V Saxena","year":"2006","unstructured":"Saxena V, Orgill D, Kohane I: Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res 2006, 34: e151. 10.1093\/nar\/gkl766","journal-title":"Nucleic Acids Res"},{"key":"2891_CR20","doi-asserted-by":"publisher","first-page":"1356","DOI":"10.1093\/bioinformatics\/btm116","volume":"23","author":"DM Kemp","year":"2007","unstructured":"Kemp DM, Nirmala NR, Szustakowski JD: Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation. Bioinformatics 2007, 23: 1356\u201362. 10.1093\/bioinformatics\/btm116","journal-title":"Bioinformatics"},{"key":"2891_CR21","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1038\/nm733","volume":"8","author":"DG Beer","year":"2002","unstructured":"Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, et al.: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 8: 816\u201324.","journal-title":"Nat Med"},{"key":"2891_CR22","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, et al.: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 2001, 98: 13790\u20135. 10.1073\/pnas.191502998","journal-title":"Proc Natl Acad Sci USA"},{"key":"2891_CR23","unstructured":"The Molecular Signature Database[http:\/\/www.broad.mit.edu\/gsea\/msigdb\/]"},{"key":"2891_CR24","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1038\/nrc2069","volume":"7","author":"RT Dorsam","year":"2007","unstructured":"Dorsam RT, Gutkind JS: G-protein-coupled receptors and cancer. Nat Rev Cancer 2007, 7: 79\u201394. 10.1038\/nrc2069","journal-title":"Nat Rev Cancer"},{"key":"2891_CR25","first-page":"1329","volume":"27","author":"S Li","year":"2005","unstructured":"Li S, Huang S, Peng SB: Overexpression of G protein-coupled receptors in cancer cells: involvement in tumor progression. Int J Oncol 2005, 27: 1329\u201339.","journal-title":"Int J Oncol"},{"key":"2891_CR26","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1016\/j.clon.2007.04.002","volume":"19","author":"G Altiay","year":"2007","unstructured":"Altiay G, Ciftci A, Demir M, Kocak Z, Sut N, Tabakoglu E, Hatipoglu ON, Caglar T: High plasma D-dimer level is associated with decreased survival in patients with lung cancer. Clin Oncol (R Coll Radiol) 2007, 19: 494\u20138.","journal-title":"Clin Oncol (R Coll Radiol)"},{"key":"2891_CR27","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1016\/j.lungcan.2006.03.015","volume":"53","author":"D Antoniou","year":"2006","unstructured":"Antoniou D, Pavlakou G, Stathopoulos GP, Karydis I, Chondrou E, Papageorgiou C, Dariotaki F, Chaimala D, Veslemes M: Predictive value of D-dimer plasma levels in response and progressive disease in patients with lung cancer. Lung Cancer 2006, 53: 205\u201310. 10.1016\/j.lungcan.2006.03.015","journal-title":"Lung Cancer"},{"key":"2891_CR28","doi-asserted-by":"publisher","first-page":"1313","DOI":"10.1002\/cncr.22922","volume":"110","author":"PR Montgrain","year":"2007","unstructured":"Montgrain PR, Quintana R, Rascon Y, Burton DW, Deftos LJ, Casillas A, Hastings RH: Parathyroid hormone-related protein varies with sex and androgen status in nonsmall cell lung cancer. Cancer 2007, 110: 1313\u201320. 10.1002\/cncr.22922","journal-title":"Cancer"},{"key":"2891_CR29","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1476-4598-1-5","volume":"1","author":"GE Hidalgo","year":"2002","unstructured":"Hidalgo GE, Zhong L, Doherty DE, Hirschowitz EA: Plasma PGE-2 levels and altered cytokine profiles in adherent peripheral blood mononuclear cells in non-small cell lung cancer (NSCLC). Mol Cancer 2002, 1: 5. 10.1186\/1476-4598-1-5","journal-title":"Mol Cancer"},{"key":"2891_CR30","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.1126\/science.8197455","volume":"264","author":"JE Darnell Jr","year":"1994","unstructured":"Darnell JE Jr, Kerr IM, Stark GR: Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science 1994, 264: 1415\u201321. 10.1126\/science.8197455","journal-title":"Science"},{"key":"2891_CR31","doi-asserted-by":"publisher","first-page":"33637","DOI":"10.1074\/jbc.M301053200","volume":"278","author":"AS Kristof","year":"2003","unstructured":"Kristof AS, Marks-Konczalik J, Billings E, Moss J: Stimulation of signal transducer and activator of transcription-1 (STAT1)-dependent gene transcription by lipopolysaccharide and interferon-gamma is regulated by mammalian target of rapamycin. J Biol Chem 2003, 278: 33637\u201344. 10.1074\/jbc.M301053200","journal-title":"J Biol Chem"},{"key":"2891_CR32","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1083\/jcb.200211021","volume":"161","author":"P Rajan","year":"2003","unstructured":"Rajan P, Panchision DM, Newell LF, McKay RD: BMPs signal alternately through a SMAD or FRAP-STAT pathway to regulate fate choice in CNS stem cells. J Cell Biol 2003, 161: 911\u201321. 10.1083\/jcb.200211021","journal-title":"J Cell Biol"},{"key":"2891_CR33","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1476-4598-6-71","volume":"6","author":"K Fujita","year":"2007","unstructured":"Fujita K, Janz S: Attenuation of WNT signaling by DKK-1 and -2 regulates BMP2-induced osteoblast differentiation and expression of OPG, RANKL and M-CSF. Mol Cancer 2007, 6: 71. 10.1186\/1476-4598-6-71","journal-title":"Mol Cancer"},{"key":"2891_CR34","doi-asserted-by":"publisher","first-page":"1842","DOI":"10.1359\/jbmr.2003.18.10.1842","volume":"18","author":"G Rawadi","year":"2003","unstructured":"Rawadi G, Vayssiere B, Dunn F, Baron R, Roman-Roman S: BMP-2 controls alkaline phosphatase expression and osteoblast mineralization by a Wnt autocrine loop. J Bone Miner Res 2003, 18: 1842\u201353. 10.1359\/jbmr.2003.18.10.1842","journal-title":"J Bone Miner Res"},{"key":"2891_CR35","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/1471-2164-8-70","volume":"8","author":"B Kulterer","year":"2007","unstructured":"Kulterer B, Friedl G, Jandrositz A, Sanchez-Cabo F, Prokesch A, Paar C, Scheideler M, Windhager R, Preisegger KH, Trajanoski Z: Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation. BMC Genomics 2007, 8: 70. 10.1186\/1471-2164-8-70","journal-title":"BMC Genomics"},{"key":"2891_CR36","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1002\/jcb.10515","volume":"89","author":"E Balint","year":"2003","unstructured":"Balint E, Lapointe D, Drissi H, Meijden C, Young DW, van Wijnen AJ, Stein JL, Stein GS, Lian JB: Phenotype discovery by gene expression profiling: mapping of biological processes linked to BMP-2-mediated osteoblast differentiation. J Cell Biochem 2003, 89: 401\u201326. 10.1002\/jcb.10515","journal-title":"J Cell Biochem"},{"key":"2891_CR37","doi-asserted-by":"publisher","first-page":"5676","DOI":"10.1038\/sj.onc.1208920","volume":"24","author":"J Larsson","year":"2005","unstructured":"Larsson J, Karlsson S: The role of Smad signaling in hematopoiesis. Oncogene 2005, 24: 5676\u201392. 10.1038\/sj.onc.1208920","journal-title":"Oncogene"},{"key":"2891_CR38","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/S0014-4827(02)00013-7","volume":"282","author":"V Maguer-Satta","year":"2003","unstructured":"Maguer-Satta V, Bartholin L, Jeanpierre S, Ffrench M, Martel S, Magaud JP, Rimokh R: Regulation of human erythropoiesis by activin A, BMP2, and BMP4, members of the TGFbeta family. Exp Cell Res 2003, 282: 110\u201320. 10.1016\/S0014-4827(02)00013-7","journal-title":"Exp Cell Res"},{"key":"2891_CR39","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1002\/path.1785","volume":"206","author":"MW Helms","year":"2005","unstructured":"Helms MW, Packeisen J, August C, Schittek B, Boecker W, Brandt BH, Buerger H: First evidence supporting a potential role for the BMP\/SMAD pathway in the progression of oestrogen receptor-positive breast cancer. J Pathol 2005, 206: 366\u201376. 10.1002\/path.1785","journal-title":"J Pathol"},{"key":"2891_CR40","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1359\/JBMR.0301249","volume":"19","author":"DB Ong","year":"2004","unstructured":"Ong DB, Colley SM, Norman MR, Kitazawa S, Tobias JH: Transcriptional regulation of a BMP-6 promoter by estrogen receptor alpha. J Bone Miner Res 2004, 19: 447\u201354. 10.1359\/JBMR.0301249","journal-title":"J Bone Miner Res"},{"key":"2891_CR41","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1093\/bioinformatics\/btl599","volume":"23","author":"Z Jiang","year":"2007","unstructured":"Jiang Z, Gentleman R: Extensions to gene set enrichment. Bioinformatics 2007, 23: 306\u201313. 10.1093\/bioinformatics\/btl599","journal-title":"Bioinformatics"},{"key":"2891_CR42","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the False Discovery Rate \u2013 a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 1995, 57: 289\u2013300.","journal-title":"Journal of the Royal Statistical Society Series B-Methodological"},{"key":"2891_CR43","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1146\/annurev.ps.46.020195.003021","volume":"46","author":"JP Shaffer","year":"1995","unstructured":"Shaffer JP: Multiple Hypothesis-Testing. Annu Rev Psychol 1995, 46: 561\u2013584. 10.1146\/annurev.ps.46.020195.003021","journal-title":"Annu Rev Psychol"},{"key":"2891_CR44","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1080\/02664769823304","volume":"25","author":"JM Stonehouse","year":"1998","unstructured":"Stonehouse JM, Forrester GJ: Robustness of the t and U tests under combined assumption violations. Journal of Applied Statistics 1998, 25: 63\u201374. 10.1080\/02664769823304","journal-title":"Journal of Applied Statistics"},{"key":"2891_CR45","doi-asserted-by":"publisher","first-page":"124","DOI":"10.2307\/2683975","volume":"35","author":"WJ Conover","year":"1981","unstructured":"Conover WJ, Iman RL: Rank Transformations as a Bridge between Parametric and Nonparametric Statistics. American Statistician 1981, 35: 124\u2013129. 10.2307\/2683975","journal-title":"American Statistician"},{"key":"2891_CR46","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1186\/1471-2105-9-303","volume":"9","author":"K Strimmer","year":"2008","unstructured":"Strimmer K: A unified approach to false discovery rate estimation. BMC Bioinformatics 2008, 9: 303. 10.1186\/1471-2105-9-303","journal-title":"BMC Bioinformatics"},{"key":"2891_CR47","unstructured":"GAGE R package[http:\/\/sysbio.engin.umich.edu\/~luow\/downloads.php]"},{"key":"2891_CR48","unstructured":"Gene Annotation & Information Query (GAIQ)[http:\/\/sysbio.engin.umich.edu\/~luow\/project\/geneInfo.php]"},{"key":"2891_CR49","unstructured":"GSEA software[http:\/\/www.broad.mit.edu\/gsea\/downloads.jsp]"},{"key":"2891_CR50","doi-asserted-by":"publisher","first-page":"3171","DOI":"10.1158\/0008-5472.CAN-06-4571","volume":"67","author":"KA Furge","year":"2007","unstructured":"Furge KA, Chen J, Koeman J, Swiatek P, Dykema K, Lucin K, Kahnoski R, Yang XJ, Teh BT: Detection of DNA copy number changes and oncogenic signaling abnormalities from gene expression data reveals MYC activation in high-grade papillary renal cell carcinoma. Cancer Res 2007, 67: 3171\u20136. 10.1158\/0008-5472.CAN-06-4571","journal-title":"Cancer Res"},{"key":"2891_CR51","unstructured":"ChipperDB type 2 diabetes data set[http:\/\/www.diabetesgenome.org\/chipperdb\/expt.cgi?id=54]"},{"key":"2891_CR52","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","volume":"20","author":"L Gautier","year":"2004","unstructured":"Gautier L, Cope L, Bolstad BM, Irizarry RA: affy\u2013analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20: 307\u201315. 10.1093\/bioinformatics\/btg405","journal-title":"Bioinformatics"},{"key":"2891_CR53","doi-asserted-by":"publisher","first-page":"e175","DOI":"10.1093\/nar\/gni179","volume":"33","author":"M Dai","year":"2005","unstructured":"Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, et al.: Evolving gene\/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33: e175. 10.1093\/nar\/gni179","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-161.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,9]],"date-time":"2025-02-09T18:40:37Z","timestamp":1739126437000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-161"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,27]]},"references-count":53,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2891"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-161","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,5,27]]},"assertion":[{"value":"26 June 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 May 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 May 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"161"}}