ArticleJournal of bioinformatics and computational biology2015
ExAtlas: An interactive online tool for meta-analysis of gene expression data.
Article in Journal of bioinformatics and computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed, 3 syntheses or guidelines pooled it, 72 citations in OpenAlex.
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- The role of PI3K signaling pathway and its associated genes in papillary thyroid cancer.Journal of the Egyptian National Cancer Institute · 2021Pooled it
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- Gene expression in immune cells infected with Orientia tsutsugamushi and the antigenic variability of 56-kDa type-specific antigen.Scientific reports · 2026Article
- Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells.Immunity · 2026Article
- Meta-Analysis of Gene Expression Reveals the Core Transcriptomic Profile of Lesional Scalp in Alopecia Areata.Dermatology and therapy · 2025Review
- Phase separated condensates of ATRX regulate neural progenitor identity.Nature communications · 2025Article
- The role of MAPK, notch and Wnt signaling pathways in papillary thyroid cancer: Evidence from a systematic review and meta-analyzing microarray datasets employing bioinformatics knowledge and literature.Biochemistry and biophysics reports · 2024Article
- Cancer stem cells as the source of tumor associated myoepithelial cells in the tumor microenvironment developing ductal carcinoma in situ.Biomaterials · 2023Article
- Mesenchymal properties of iPSC-derived neural progenitors that generate undesired grafts after transplantation.Communications biology · 2023Article
- Biochemical, pharmacological, and toxicological attributes of caper (Food science & nutrition · 2022Article
- Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells.BMC bioinformatics · 2022Article
- Exploration of Potential Biomarker Genes and Pathways in Kawasaki Disease: An IntegratedFrontiers in genetics · 2022Article
- A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine.Briefings in bioinformatics · 2021Article
- Synthetic mRNA-based differentiation method enables early detection of Parkinson's phenotypes in neurons derived from Gaucher disease-induced pluripotent stem cells.Stem cells translational medicine · 2021Article
- Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity.Cell systems · 2020Article
- Histone deacetylase inhibitors induce medulloblastoma cell death independent of HDACs recruited in REST repression complexes.Molecular genetics & genomic medicine · 2020Article
- Understanding the Molecular Mechanisms of Asthma through Transcriptomics.Allergy, asthma & immunology research · 2020Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.