title: ExAtlas: An interactive online tool for meta-analysis of gene expression data.
abstract: We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users' own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher's methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data sets (e.g. GNF/BioGPS, Gene Ontology, KEGG, GAD phenotypes, BrainScan, ENCODE ChIP-seq, and protein-protein interaction) are pre-loaded and can be used for functional annotations.
authors.affiliation: * Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
authors.forename: Alexei A
authors.initials: AA
authors.lastname: Sharov
authors.affiliation: * Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
authors.forename: David
authors.initials: D
authors.lastname: Schlessinger
authors.affiliation: † Department of Systems Medicine, The Sakaguchi Laboratory, Keio University School of Medicine, Tokyo 160-8582, Japan.
authors.forename: Minoru S H
authors.initials: MS
authors.lastname: Ko
mesh_terms: D000704:Analysis of Variance; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D063990:Gene Ontology; D021621:Imaging, Three-Dimensional; D020407:Internet; D015201:Meta-Analysis as Topic; D012984:Software; D057188:Workflow
keywords: ANOVA; Meta-analysis; PCA; correlation matrix; expected proportion of false positives; gene set enrichment