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

Alexei A. Sharov, David Schlessinger, Minoru Ko

Research output: Contribution to journalArticle

20 Citations (Scopus)

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.

Original languageEnglish
Article number1550019
JournalJournal of Bioinformatics and Computational Biology
Volume13
Issue number6
DOIs
Publication statusPublished - 2015 Dec 1

Fingerprint

Gene expression
Meta-Analysis
Gene Ontology
Genes
Transcriptome
Gene Expression
Software
Molecular Sequence Annotation
Passive Cutaneous Anaphylaxis
Three-Dimensional Imaging
Ontology
Analysis of Variance
Proteins
Databases
Phenotype
Analysis of variance (ANOVA)
Datasets
Statistical methods
Visualization

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

ExAtlas : An interactive online tool for meta-analysis of gene expression data. / Sharov, Alexei A.; Schlessinger, David; Ko, Minoru.

In: Journal of Bioinformatics and Computational Biology, Vol. 13, No. 6, 1550019, 01.12.2015.

Research output: Contribution to journalArticle

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