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J Bioinform Comput Biol. 2015 Dec;13(6):1550019. doi: 10.1142/S0219720015500195. Epub 2015 Jun 9.

ExAtlas: An interactive online tool for meta-analysis of gene expression data.

Author information

1
* Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
2
† Department of Systems Medicine, The Sakaguchi Laboratory, Keio University School of Medicine, Tokyo 160-8582, Japan.

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.

KEYWORDS:

ANOVA; Meta-analysis; PCA; correlation matrix; expected proportion of false positives; gene set enrichment

PMID:
26223199
PMCID:
PMC5518779
DOI:
10.1142/S0219720015500195
[Indexed for MEDLINE]
Free PMC Article

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