{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T00:24:37Z","timestamp":1765758277646,"version":"3.38.0"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"S9","license":[{"start":{"date-parts":[[2010,10,1]],"date-time":"2010-10-01T00:00:00Z","timestamp":1285891200000},"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":[[2010,10]]},"DOI":"10.1186\/1471-2105-11-s9-s6","type":"journal-article","created":{"date-parts":[[2010,10,28]],"date-time":"2010-10-28T18:15:42Z","timestamp":1288289742000},"source":"Crossref","is-referenced-by-count":19,"title":["Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants"],"prefix":"10.1186","volume":"11","author":[{"given":"Alexander A","family":"Morgan","sequence":"first","affiliation":[]},{"given":"Purvesh","family":"Khatri","sequence":"additional","affiliation":[]},{"given":"Richard Hayden","family":"Jones","sequence":"additional","affiliation":[]},{"given":"Minnie M","family":"Sarwal","sequence":"additional","affiliation":[]},{"given":"Atul J","family":"Butte","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,10,28]]},"reference":[{"issue":"Suppl 1","key":"4268_CR1","doi-asserted-by":"publisher","first-page":"i84","DOI":"10.1093\/bioinformatics\/btg1010","volume":"19","author":"JK Choi","year":"2003","unstructured":"Choi JK, Yu U, Kim S, Yoo OJ: Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19(Suppl 1):i84\u201390. 10.1093\/bioinformatics\/btg1010","journal-title":"Bioinformatics"},{"key":"4268_CR2","doi-asserted-by":"crossref","unstructured":"DeConde RP, Hawley S, Falton S, Clegg N, Knudsen B, Etzioni R: \"Combining Results of Microarray Experiments: Rank Aggregation Approach\". Statistical Applications in Genetics and Molecular Biology 2006., 5(1): 10.2202\/1544-6115.1204","DOI":"10.2202\/1544-6115.1204"},{"issue":"21","key":"4268_CR3","doi-asserted-by":"publisher","first-page":"2910","DOI":"10.1093\/bioinformatics\/btm483","volume":"23","author":"SB English","year":"2007","unstructured":"English SB, Butte AJ: Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. Bioinformatics 2007, 23(21):2910\u20132917. 10.1093\/bioinformatics\/btm483","journal-title":"Bioinformatics"},{"issue":"9","key":"4268_CR4","doi-asserted-by":"publisher","first-page":"e184","DOI":"10.1371\/journal.pmed.0050184","volume":"5","author":"A Ramasamy","year":"2008","unstructured":"Ramasamy A, Mondry A, Holmes CC, Altman DG: Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008, 5(9):e184. 10.1371\/journal.pmed.0050184","journal-title":"PLoS Med"},{"key":"4268_CR5","first-page":"4427","volume":"62","author":"DR Rhodes","year":"2002","unstructured":"Rhodes DR, Barrette TR, Rubin MA, Ghost D, Chinnaaiyan AM: Meta-Analysis of Microarrays: Interstudy Validation of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer. Cancer Res 2002, 62: 4427\u20134433.","journal-title":"Cancer Res"},{"issue":"3","key":"4268_CR6","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/bioinformatics\/btm620","volume":"24","author":"F Hong","year":"2008","unstructured":"Hong F, Breitling R: A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 2008, 24(3):374\u2013382. 10.1093\/bioinformatics\/btm620","journal-title":"Bioinformatics"},{"key":"4268_CR7","unstructured":"Number of U.S. Transplants Per Year, 1988\u20132008[ http:\/\/www.infoplease.com\/science\/health\/us-transplants-year-1988\u20132007.html ]"},{"key":"4268_CR8","volume-title":"Statistical methods for meta-analysis","author":"L Hedges","year":"1985","unstructured":"Hedges L, Olkin I: Statistical methods for meta-analysis. 1985."},{"issue":"16","key":"4268_CR9","doi-asserted-by":"publisher","first-page":"9440","DOI":"10.1073\/pnas.1530509100","volume":"100","author":"JD Storey","year":"2003","unstructured":"Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003, 100(16):9440\u20139445. 10.1073\/pnas.1530509100","journal-title":"Proc Natl Acad Sci U S A"},{"key":"4268_CR10","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1985","unstructured":"Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 1985, 57: 289\u2013300.","journal-title":"Journal of the Royal Statistical Society Series B"},{"key":"4268_CR11","volume-title":"A comparison of fold-change and the t-statistic for microarray data analysis","author":"D Witten","year":"2007","unstructured":"Witten D, Tibshirani R: A comparison of fold-change and the t-statistic for microarray data analysis. Stanford University; 2007."},{"issue":"9","key":"4268_CR12","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nbt1239","volume":"24","author":"L Shi","year":"2006","unstructured":"Shi L, al e: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24(9):1151\u20131161. 10.1038\/nbt1239","journal-title":"Nat Biotechnol"},{"issue":"4","key":"4268_CR13","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/gb-2003-4-4-210","volume":"4","author":"X Cui","year":"2003","unstructured":"Cui X, Churchill G: Statistical tests for differential expression in cDNA microarray experiments. Genome biology 2003, 4(4):210. 10.1186\/gb-2003-4-4-210","journal-title":"Genome biology"},{"issue":"4","key":"4268_CR14","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/gb-2003-4-4-210","volume":"4","author":"X Cui","year":"2003","unstructured":"Cui X, Churchill GA: Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 2003, 4(4):210. 10.1186\/gb-2003-4-4-210","journal-title":"Genome Biol"},{"issue":"43","key":"4268_CR15","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 U S A 2005, 102(43):15545\u201315550. 10.1073\/pnas.0506580102","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"4268_CR16","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1111\/j.1600-6143.2008.02512.x","volume":"9","author":"S Rodder","year":"2009","unstructured":"Rodder S, Scherer A, Raulf F, Berthier CC, Hertig A, Couzi L, Durrbach A, Rondeau E, Marti HP: Renal allografts with IF\/TA display distinct expression profiles of metzincins and related genes. Am J Transplant 2009, 9(3):517\u2013526. 10.1111\/j.1600-6143.2008.02512.x","journal-title":"Am J Transplant"},{"issue":"9","key":"4268_CR17","doi-asserted-by":"publisher","first-page":"1475","DOI":"10.1111\/j.1600-6143.2004.00526.x","volume":"4","author":"SM Flechner","year":"2004","unstructured":"Flechner SM, Kurian SM, Head SR, Sharp SM, Whisenant TC, Zhang J, Chismar JD, Horvath S, Mondala T, Gilmartin T, et al.: Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes. Am J Transplant 2004, 4(9):1475\u20131489. 10.1111\/j.1600-6143.2004.00526.x","journal-title":"Am J Transplant"},{"issue":"10","key":"4268_CR18","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1164\/rccm.200305-644OC","volume":"168","author":"VJ Gimino","year":"2003","unstructured":"Gimino VJ, Lande JD, Berryman TR, King RA, Hertz MI: Gene expression profiling of bronchoalveolar lavage cells in acute lung rejection. Am J Respir Crit Care Med 2003, 168(10):1237\u20131242. 10.1164\/rccm.200305-644OC","journal-title":"Am J Respir Crit Care Med"},{"issue":"2","key":"4268_CR19","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1097\/TP.0b013e318160268a","volume":"85","author":"J Patil","year":"2008","unstructured":"Patil J, Lande JD, Li N, Berryman TR, King RA, Hertz MI: Bronchoalveolar lavage cell gene expression in acute lung rejection: development of a diagnostic classifier. Transplantation 2008, 85(2):224\u2013231. 10.1097\/TP.0b013e318160268a","journal-title":"Transplantation"},{"key":"4268_CR20","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/1471-2261-6-29","volume":"6","author":"K Karason","year":"2006","unstructured":"Karason K, Jernas M, Hagg DA, Svensson PA: Evaluation of CXCL9 and CXCL10 as circulating biomarkers of human cardiac allograft rejection. BMC Cardiovasc Disord 2006, 6: 29. 10.1186\/1471-2261-6-29","journal-title":"BMC Cardiovasc Disord"},{"issue":"Database issue","key":"4268_CR21","doi-asserted-by":"publisher","first-page":"D760","DOI":"10.1093\/nar\/gkl887","volume":"35","author":"T Barrett","year":"2007","unstructured":"Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res 2007, 35(Database issue):D760\u2013765. 10.1093\/nar\/gkl887","journal-title":"Nucleic Acids Res"},{"key":"4268_CR22","doi-asserted-by":"publisher","DOI":"10.1007\/0-387-29362-0","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"R Gentleman","year":"2005","unstructured":"Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer-Verlag; 2005."},{"issue":"Database issue","key":"4268_CR23","doi-asserted-by":"publisher","first-page":"D5","DOI":"10.1093\/nar\/gkl1031","volume":"35","author":"DL Wheeler","year":"2007","unstructured":"Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007, 35(Database issue):D5\u201312. 10.1093\/nar\/gkl1031","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"4268_CR24","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1038\/nmeth1107-879","volume":"4","author":"R Chen","year":"2007","unstructured":"Chen R, Li L, Butte AJ: AILUN: reannotating gene expression data automatically. Nat Methods 2007, 4(11):879. 10.1038\/nmeth1107-879","journal-title":"Nat Methods"},{"issue":"20","key":"4268_CR25","doi-asserted-by":"publisher","first-page":"3940","DOI":"10.1093\/bioinformatics\/bti623","volume":"21","author":"T Sing","year":"2005","unstructured":"Sing T, Sander O, Beerenwinkel N, Lengauer T: ROCR: visualizing classifier performance in R. Bioinformatics 2005, 21(20):3940\u20133941. 10.1093\/bioinformatics\/bti623","journal-title":"Bioinformatics"},{"key":"4268_CR26","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"KS Pollard","year":"2005","unstructured":"Pollard KS, Dudoit S, van der Laan MJ: Multiple Testing Procedures: the multtest Package and Applications to Genomics. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Edited by: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S. New York: Springer; 2005."},{"key":"4268_CR27","first-page":"424","volume-title":"Journal of the American Statistical Association","author":"D Carr","year":"1987","unstructured":"Carr D, Littlefield R, Nicholson W, Littlefield J: Scatterplot matrix techniques for large N. Journal of the American Statistical Association 1987, 424\u2013436. 10.2307\/2289444"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S9-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-S9-S6\/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-S9-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T10:53:14Z","timestamp":1740653594000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-S9-S6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10]]},"references-count":27,"journal-issue":{"issue":"S9","published-print":{"date-parts":[[2010,10]]}},"alternative-id":["4268"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-s9-s6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2010,10]]},"article-number":"S6"}}