ArticlePloS one2020
All of gene expression (AOE): An integrated index for public gene expression databases.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Identification of drug responsible glycogene signature in liver carcinoma from meta-analysis using RNA-seq data.Glycoconjugate journal · 2024Pooled it
- Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites.International journal of molecular sciences · 2023Pooled it
- A comprehensive analysis of mRNA expression profiles of Esophageal Squamous Cell Carcinoma reveals downregulation of Desmoglein 1 and crucial genomic targets.Cancer biomarkers : section A of Disease markers · 2023Pooled it
- Data Mining of Microarray Datasets in Translational Neuroscience.Brain sciences · 2023Review
- Global comparative transcriptomes uncover novel and population-specific gene expression in esophageal squamous cell carcinoma.Infectious agents and cancer · 2023Article
- Bioinformatics for wet-lab scientists: practical application in sequencing analysis.BMC genomics · 2023Article
- Enhancing untargeted metabolomics using metadata-based source annotation.Nature biotechnology · 2022Article
- Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities.Chemical research in toxicology · 2022Review
- Article
- Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia.Life (Basel, Switzerland) · 2022Article
- Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes.Biomedicines · 2021Article
- ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress.Biology · 2021Article
- Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival.International journal of molecular sciences · 2021Article
- Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes.Biomedicines · 2021Article
- Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice.Mechanisms of ageing and development · 2021Article
- Meta-Analysis of Oxidative Transcriptomes in Insects.Antioxidants (Basel, Switzerland) · 2021Article
- Meta-Analysis of Hypoxic Transcriptomes from Public Databases.Biomedicines · 2020Article
- DDBJ Database updates and computational infrastructure enhancement.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.
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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.