Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases.docVIP

BMC Genomics BioMedCentral Methodology article Open Access Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases Lukasz Huminiecki*, Andrew T Lloyd and Kenneth H Wolfe Address: Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland Email: Lukasz Huminiecki* - huminiel@tcd.ie; Andrew T Lloyd - atlloyd@tcd.ie; Kenneth H Wolfe - khwolfe@tcd.ie * Corresponding author Published: 29 July 2003 Received: 20 January 2003 Accepted: 29 July 2003 BMC Genomics 2003, 4:31 This article is available from: /1471-2164/4/31 ? 2003 Huminiecki et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. Abstract Background: Extracting biological knowledge from large amounts of gene expression information deposited in public databases is a major challenge of the postgenomic era. Additional insights may be derived by data integration and cross-platform comparisons of expression profiles. However, database meta-analysis is complicated by differences in experimental technologies, data post- processing, database formats, and inconsistent gene and sample annotation. Results: We have analysed expression profiles from three public databases: Gene Expression Atlas, SAGEmap and TissueInfo. These are repositories of oligonucleotide microarray, Serial Analysis of Gene Expression and Expressed Sequence Tag human gene expression data respectively. We devised a method, Preferential Expression Measure, to identify genes that are significantly over- or under-expressed in any given tissue. We examined intra- and inter-database consistency of Preferential Expression Measures. There was good correlation between replicate experiments of oligonucleotide micr