{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T12:45:15Z","timestamp":1722689115619},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,12,1]],"date-time":"2009-12-01T00:00:00Z","timestamp":1259625600000},"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":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-431","type":"journal-article","created":{"date-parts":[[2009,12,18]],"date-time":"2009-12-18T20:42:41Z","timestamp":1261168961000},"source":"Crossref","is-referenced-by-count":4,"title":["Discovering collectively informative descriptors from high-throughput experiments"],"prefix":"10.1186","volume":"10","author":[{"given":"Clark D","family":"Jeffries","sequence":"first","affiliation":[]},{"given":"William O","family":"Ward","sequence":"additional","affiliation":[]},{"given":"Diana O","family":"Perkins","sequence":"additional","affiliation":[]},{"given":"Fred A","family":"Wright","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,12,18]]},"reference":[{"key":"3161_CR1","unstructured":"Fisher's Exact Test[ http:\/\/www.langsrud.com\/fisher.htm ]"},{"key":"3161_CR2","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1080\/02664760701594246","volume":"34","author":"\u00d8 Langsrud","year":"2007","unstructured":"Langsrud \u00d8, J\u00f8rgensen K, Ofstad R, N\u00e6s T: Analyzing Designed Experiments with Multiple Responses. Journal of Applied Statistics 2007, 34: 1275\u20131296. 10.1080\/02664760701594246","journal-title":"Journal of Applied Statistics"},{"key":"3161_CR3","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1136\/bmj.320.7249.1574","volume":"320","author":"AJ Sutton","year":"2000","unstructured":"Sutton AJ, Duval SJ, Tweedie RL, Abrams KR, Jones DR: Empirical assessment of effect of publication bias on meta-analyses. BMJ 2000, 320: 1574\u20131547. 10.1136\/bmj.320.7249.1574","journal-title":"BMJ"},{"key":"3161_CR4","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1186\/1471-2164-8-96","volume":"8","author":"A Hess","year":"2007","unstructured":"Hess A, Iyer H: Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays. BMC Genomics 2007, 8: 96. 10.1186\/1471-2164-8-96","journal-title":"BMC Genomics"},{"key":"3161_CR5","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1126\/science.1132939","volume":"313","author":"J Lamb","year":"2006","unstructured":"Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ, Clemons PA, Wei R, Carr SA, Lander ES, Golub TR: The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006, 313: 1929\u20131935. 10.1126\/science.1132939","journal-title":"Science"},{"key":"3161_CR6","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1023\/A:1025386326946","volume":"17","author":"A Golbraikh","year":"2003","unstructured":"Golbraikh A, Shen M, Xiao Z, Xiao YD, Lee KH, Tropsha A: Rational selection of training and test sets for the development of validated QSAR models. J Comput Aided Mol Des 2003, 17: 241\u2013253. 10.1023\/A:1025386326946","journal-title":"J Comput Aided Mol Des"},{"key":"3161_CR7","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/0471266949.bmc002","volume-title":"Burger's Medicinal Chemistry and Drug Discovery","author":"A Tropsha","year":"2003","unstructured":"Tropsha A: Recent Trends in Quantitative Structure-Activity Relationships. In Burger's Medicinal Chemistry and Drug Discovery. Edited by: Abraham D. New York: John Wiley & Sons, Inc; 2003:49\u201377."},{"key":"3161_CR8","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1021\/jm040835a","volume":"48","author":"J Kazius","year":"2005","unstructured":"Kazius J, McGuire R, Bursi R: Derivation and validation of toxicophores for mutagenicity prediction. J Med Chem 2005, 48: 312\u2013320. 10.1021\/jm040835a","journal-title":"J Med Chem"},{"key":"3161_CR9","unstructured":"Gene Expression Omnibus[ http:\/\/www.ncbi.nlm.nih.gov\/geo\/ ]"},{"key":"3161_CR10","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30: 207\u2013210. 10.1093\/nar\/30.1.207","journal-title":"Nucleic Acids Res"},{"key":"3161_CR11","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1016\/S0076-6879(06)11019-8","volume":"411","author":"T Barrett","year":"2006","unstructured":"Barrett T, Edgar R: Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 2006, 411: 352\u201369. 10.1016\/S0076-6879(06)11019-8","journal-title":"Methods Enzymol"},{"key":"3161_CR12","unstructured":"Oncomine[ http:\/\/www.oncomine.org\/ ]"},{"key":"3161_CR13","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1593\/neo.07112","volume":"9","author":"DR Rhodes","year":"2007","unstructured":"Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM: Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007, 9: 166\u2013180. 10.1593\/neo.07112","journal-title":"Neoplasia"},{"key":"3161_CR14","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/nature03552","volume":"435","author":"L He","year":"2005","unstructured":"He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM: A microRNA polycistron as a potential human oncogene. Nature 2005, 435: 828\u2013833. 10.1038\/nature03552","journal-title":"Nature"},{"key":"3161_CR15","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature07228","volume":"455","author":"M Selbach","year":"2008","unstructured":"Selbach M, Schwanh\u00e4usser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N: Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455: 58\u201363. 10.1038\/nature07228","journal-title":"Nature"},{"key":"3161_CR16","doi-asserted-by":"publisher","first-page":"2070","DOI":"10.1038\/sj.mt.6300311","volume":"15","author":"HS Soifer","year":"2007","unstructured":"Soifer HS, Rossi JJ, Saetrom P: MicroRNAs in disease and potential therapeutic applications. Mol Ther 2007, 15: 2070\u20132079. 10.1038\/sj.mt.6300311","journal-title":"Mol Ther"},{"key":"3161_CR17","doi-asserted-by":"publisher","first-page":"1763","DOI":"10.1016\/S0002-9440(10)61257-6","volume":"167","author":"RS Stearman","year":"2005","unstructured":"Stearman RS, Dwyer-Nield L, Zerbe L, Blaine SA, Chan Z, Bunn PA Jr, Johnson GL, Hirsch FR, Merrick DT, Franklin WA, Baron AE, Keith RL, Nemenoff RA, Malkinson AM, Geraci MW: Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen-induced murine model. Am J Pathol 2005, 167: 1763\u20131775.","journal-title":"Am J Pathol"},{"key":"3161_CR18","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. PNAS 2001, 98: 13790\u201313795. 10.1073\/pnas.191502998","journal-title":"PNAS"},{"issue":"Suppl 3","key":"3161_CR19","doi-asserted-by":"publisher","first-page":"6S","DOI":"10.1378\/chest.121.3_suppl.6S","volume":"121","author":"CA Powell","year":"2002","unstructured":"Powell CA, Xu G, Filmus J, Busch S, Brody JS, Rothman PB: Oligonucleotide microarray analysis of lung adenocarcinoma in smokers and nonsmokers identifies GPC3 as a potential lung tumor suppressor. Chest 2002, 121(Suppl 3):6S-7S. 10.1378\/chest.121.3_suppl.6S","journal-title":"Chest"},{"key":"3161_CR20","volume-title":"Lung Cancer","author":"EP Kopantzev","year":"2008","unstructured":"Kopantzev EP, Monastyrskaya GS, Vinogradova TV, Zinovyeva MV, Kostina MB, Filyukova OB, Tonevitsky AG, Sukhikh GT, Sverdlov ED: Differences in gene expression levels between early and later stages of human lung development are opposite to those between normal lung tissue and non-small lung cell carcinoma. Lung Cancer 2008. 2008 Epub Apr 3 2008 Epub Apr 3"},{"key":"3161_CR21","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1002\/1097-0142(19880901)62:5<869::AID-CNCR2820620503>3.0.CO;2-6","volume":"62","author":"BA Jensen","year":"1988","unstructured":"Jensen BA, Clemmensen I: Plasma tetranectin is reduced in cancer and related to metastasia. Cancer 1988, 62: 869\u2013872. Publisher Full Text 10.1002\/1097-0142(19880901)62:5<869::AID-CNCR2820620503>3.0.CO;2-6","journal-title":"Cancer"},{"key":"3161_CR22","first-page":"1615","volume":"56","author":"B Millauer","year":"1996","unstructured":"Millauer B, Longhi MP, Plate KH, Shawver LK, Risau W, Ullrich A, Strawn LM: Dominant-negative inhibition of Flk-1 suppresses the growth of many tumor types in vivo. Cancer Res 1996, 56: 1615\u20131620.","journal-title":"Cancer Res"},{"key":"3161_CR23","doi-asserted-by":"publisher","first-page":"2619","DOI":"10.1161\/ATVBAHA.107.150482","volume":"27","author":"CM Findley","year":"2007","unstructured":"Findley CM, Cudmore MJ, Ahmed A, Kontos CD: VEGF induces Tie2 shedding via a phosphoinositide 3-kinase\/Akt dependent pathway to modulate Tie2 signaling. Arterioscler Thromb Vasc Biol 2007, 27: 2619\u20132626. 10.1161\/ATVBAHA.107.150482","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"3161_CR24","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1007\/s00428-003-0802-6","volume":"442","author":"B Singh","year":"2003","unstructured":"Singh B, Tschernig T, van Griensven M, Fieguth A, Pabst R: Expression of vascular adhesion protein-1 in normal and inflamed mice lungs and normal human lungs. Virchows Arch 2003, 442: 491\u2013495.","journal-title":"Virchows Arch"},{"key":"3161_CR25","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1158\/1078-0432.CCR-06-1593","volume":"13","author":"R Li","year":"2007","unstructured":"Li R, Todd NW, Qiu Q, Fan T, Zhao RY, Rodgers WH, Fang HB, Katz RL, Stass SA, Jiang F: Genetic deletions in sputum as diagnostic markers for early detection of stage I non-small cell lung cancer. Clin Cancer Res 2007, 13: 482\u2013487. 10.1158\/1078-0432.CCR-06-1593","journal-title":"Clin Cancer Res"},{"key":"3161_CR26","doi-asserted-by":"publisher","first-page":"5746","DOI":"10.1158\/1078-0432.CCR-06-0324","volume":"12","author":"GC Chang","year":"2006","unstructured":"Chang GC, Liu KJ, Hsieh CL, Hu TS, Charoenfuprasert S, Liu HK, Luh KT, Hsu LH, Wu CW, Ting CC, Chen CY, Chen KC, Yang TY, Chou TY, Wang WH, Whang-Peng J, Shih NY: Identification of alpha-enolase as an autoantigen in lung cancer: its overexpression is associated with clinical outcomes. Clin Cancer Res 2006, 12: 5746\u20135754. 10.1158\/1078-0432.CCR-06-0324","journal-title":"Clin Cancer Res"},{"key":"3161_CR27","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.prp.2005.12.003","volume":"202","author":"YH Soung","year":"2006","unstructured":"Soung YH, Lee JW, Kim SY, Nam SW, Park WS, Lee JY, Yoo NJ, Lee SH: Mutational analysis of the kinase domain of MYLK2 gene in common human cancers. Pathol Res Pract 2006, 202: 137\u2013140. 10.1016\/j.prp.2005.12.003","journal-title":"Pathol Res Pract"},{"key":"3161_CR28","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1089\/omi.2006.0004","volume":"11","author":"A Sadanandam","year":"2007","unstructured":"Sadanandam A, Varney ML, Kinarsky L, Ali H, Mosley RL, Singh RK: Identification of functional cell adhesion molecules with a potential role in metastasis by a combination of in vivo phage display and in silico analysis. OMICS 2007, 11: 41\u201357. 10.1089\/omi.2006.0004","journal-title":"OMICS"},{"key":"3161_CR29","doi-asserted-by":"publisher","first-page":"2918","DOI":"10.1158\/0008-5472.CAN-05-4003","volume":"66","author":"DA Smirnov","year":"2006","unstructured":"Smirnov DA, Foulk BW, Doyle GV, Connelly MC, Terstappen LW, O'Hara SM: Global gene expression profiling of circulating endothelial cells in patients with metastatic carcinomas. Cancer Res 2006, 66: 2918\u20132922. 10.1158\/0008-5472.CAN-05-4003","journal-title":"Cancer Res"},{"key":"3161_CR30","doi-asserted-by":"publisher","first-page":"3806","DOI":"10.1074\/jbc.272.6.3806","volume":"272","author":"AN Pronin","year":"1997","unstructured":"Pronin AN, Benovic JL: Regulation of the G protein-coupled receptor kinase GRK5 by protein kinase C. J Biol Chem 1997, 272: 3806\u20133812. 10.1074\/jbc.272.29.18273","journal-title":"J Biol Chem"},{"key":"3161_CR31","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.canlet.2007.02.018","volume":"255","author":"JS Nam","year":"2007","unstructured":"Nam JS, Hirohashi S, Wakefield LM: Dysadherin: a new player in cancer progression. Cancer Lett 2007, 255: 161\u2013169. 10.1016\/j.canlet.2007.02.018","journal-title":"Cancer Lett"},{"key":"3161_CR32","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, 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: 816\u2013824.","journal-title":"Nat Med"},{"key":"3161_CR33","volume-title":"Resampling-Based Multiple Testing: Examples and Methods for p-value Adjustment","author":"P Westfall","year":"1993","unstructured":"Westfall P, Young SS: Resampling-Based Multiple Testing: Examples and Methods for p-value Adjustment. New York: Wiley; 1993. (especially page 112) (especially page 112)"},{"key":"3161_CR34","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4899-2887-0","volume-title":"Theoretical Statistics","author":"DR Cox","year":"1974","unstructured":"Cox DR, Hinkley D: Theoretical Statistics. London: Chapman and Hall; 1974. (especially page 179) (especially page 179)"},{"key":"3161_CR35","volume-title":"A Guide to Chi-Squared Testing","author":"P Greenwood","year":"1996","unstructured":"Greenwood P, Nikulin M: A Guide to Chi-Squared Testing. Hoboken, NJ: Wiley; 1996."},{"key":"3161_CR36","volume-title":"Biostatistical analysis","author":"J Zar","year":"1999","unstructured":"Zar J: Biostatistical analysis. 4th edition. Upper Saddle River, NJ: Prentice Hall; 1999.","edition":"4"},{"key":"3161_CR37","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1007\/BF02310555","volume":"16","author":"L Cronbach","year":"1951","unstructured":"Cronbach L: Coefficient alpha and the internal structure of tests. Psychometrika 1951, 16: 297\u2013334. 10.1007\/BF02310555","journal-title":"Psychometrika"},{"key":"3161_CR38","doi-asserted-by":"publisher","first-page":"R54","DOI":"10.1186\/gb-2007-8-4-r54","volume":"8","author":"M Blangiardo","year":"2007","unstructured":"Blangiardo M, Richardson S: Statistical tools for synthesizing lists of differentially expressed features in related experiments. Genome Biol 2007, 8: R54. 10.1186\/gb-2007-8-4-r54","journal-title":"Genome Biol"},{"key":"3161_CR39","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.febslet.2004.07.055","volume":"573","author":"R Breitling","year":"2004","unstructured":"Breitling R, Armengaud P, Amtmann A, Herzyk P: Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 2004, 573: 83\u201392. 10.1016\/j.febslet.2004.07.055","journal-title":"FEBS Lett"},{"key":"3161_CR40","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1142\/S0219720005001442","volume":"3","author":"R Breitling","year":"2005","unstructured":"Breitling R, Herzyk P: Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data. J Bioinform Comput Biol 2005, 3: 1171\u20131189. 10.1142\/S0219720005001442","journal-title":"J Bioinform Comput Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-431\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T08:34:15Z","timestamp":1634373255000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-431"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["3161"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-431","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,12]]},"article-number":"431"}}