User:Matthew Whiteside/Notebook/Malaria Microarray/2009/02/09

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Performing Meta-Analysis Citations for selecting differentially-expressed genes from meta-analysis. This DE genes will be used as input into clustering algorithms. Hong F and Breitling R. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics. 2008 Feb 1;24(3):374-82. DOI:10.1093/bioinformatics/btm620 | Evaluation and discussion of DE detection in Meta-analysis. RankProd recommended. Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, and Chory J. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics. 2006 Nov 15;22(22):2825-7. DOI:10.1093/bioinformatics/btl476 | One approach for DE detection. Grützmann R, Boriss H, Ammerpohl O, Lüttges J, Kalthoff H, Schackert HK, Klöppel G, Saeger HD, and Pilarsky C. Meta-analysis of microarray data on pancreatic cancer defines a set of commonly dysregulated genes. Oncogene. 2005 Jul 28;24(32):5079-88. DOI:10.1038/sj.onc.1208696 | Gur-Dedeoglu B, Konu O, Kir S, Ozturk AR, Bozkurt B, Ergul G, and Yulug IG. A resampling-based meta-analysis for detection of differential gene expression in breast cancer. BMC Cancer. 2008 Dec 30;8:396. DOI:10.1186/1471-2407-8-396 | Jung YY, Oh MS, Shin DW, Kang SH, and Oh HS. Identifying differentially expressed genes in meta-analysis via Bayesian model-based clustering. Biom J. 2006 Jun;48(3):435-50. DOI:10.1002/bimj.200410230 | Ma S and Huang J. Regularized gene selection in cancer microarray meta-analysis. BMC Bioinformatics. 2009 Jan 1;10:1. DOI:10.1186/1471-2105-10-1 | Method for selecting associated genes from multiple experiments with different setups Sohal D, Yeatts A, Ye K, Pellagatti A, Zhou L, Pahanish P, Mo Y, Bhagat T, Mariadason J, Boultwood J, Melnick A, Greally J, and Verma A. Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration. PLoS One. 2008 Aug 13;3(8):e2965. DOI:10.1371/journal.pone.0002965 | Ramasamy A, Mondry A, Holmes CC, and Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med. 2008 Sep 30;5(9):e184. DOI:10.1371/journal.pmed.0050184 | VERY GOOD!! Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G 3rd, and McCaffrey TA. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene. 2007 Oct 15;401(1-2):12-8. DOI:10.1016/j.gene.2007.06.016 | More of an opinion paper