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

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 a...

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Veröffentlicht in:Journal of bioinformatics and computational biology Jg. 13; H. 6; S. 1550019
Hauptverfasser: Sharov, Alexei A, Schlessinger, David, Ko, Minoru S H
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Singapore 01.12.2015
Schlagworte:
Analysis of Variance
Computational Biology - methods
Databases, Genetic
Gene Expression Profiling
Gene Ontology
Imaging, Three-Dimensional
Internet
Meta-Analysis as Topic
Software
Workflow
gene set enrichment
correlation matrix
ANOVA
expected proportion of false positives
Meta-analysis
PCA
ISSN:1757-6334
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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.
AbstractList 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.
Author Sharov, Alexei A
Ko, Minoru S H
Schlessinger, David
Author_xml – sequence: 1
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  surname: Sharov
  fullname: Sharov, Alexei A
  organization: Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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  givenname: David
  surname: Schlessinger
  fullname: Schlessinger, David
  organization: Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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  givenname: Minoru S H
  surname: Ko
  fullname: Ko, Minoru S H
  organization: † Department of Systems Medicine, The Sakaguchi Laboratory, Keio University School of Medicine, Tokyo 160-8582, Japan
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Keywords gene set enrichment
correlation matrix
ANOVA
expected proportion of false positives
Meta-analysis
PCA
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Snippet We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools,...
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SubjectTerms Analysis of Variance
Computational Biology - methods
Databases, Genetic
Gene Expression Profiling
Gene Ontology
Imaging, Three-Dimensional
Internet
Meta-Analysis as Topic
Software
Workflow
Title ExAtlas: An interactive online tool for meta-analysis of gene expression data
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