NCBI GEO: archive for functional genomics data sets—10 years on

By Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, K. A. Marshall, Katherine H. Phillippy, Patti M. Sherman and 5 more. Nucleic Acids Res., 2010

1,262 citations recorded by the source corpus.

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3a09814039dc1b8ed55a4c54f8425b18b26b7abd

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Citations in the corpus

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data (2012, methodology): “A total of 543 ChIP-Seq peak data sets for 252 different transcription factors were compiled from multiple related studies and downloaded from the NCBI GEO database (13), the ENCODE (14) and modENCODE (15,16) databases, or the Supplementary Data of the original research articles (Supplementary Table”
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species (2011, methodology): ““Experimental Data” (box 2) encompasses transcriptomic data (GEO [6, 7], ArrayExpress [26], and Proteomics Resource Centers [PRCs] [56]), proteomics data from mass spectrometry (Peptidome [25], PRIDE [48] and the PRCs), protein-protein interaction data from the PRCs and IntACt (4), and protein 3-”
RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome (2012, methodology): “All data have been deposited in NCBI’s GEO (16,17), and accessible through GEO series accession numbers GSE36040, GSE36042, GSE36043, GSE36044, GSE39423, GSE39424, GSE39425, GSE39426, GSE39427, GSE39429 and GSE39432.”
BioGPS: building your own mash-up of gene annotations and expression profiles (2015, methodology): “We then expanded the dataset collection by pre-loading ∼ 2000 datasets from NCBI’s GEO repository (11).”
Chipster: user-friendly analysis software for microarray and other high-throughput data (2011, methodology): “Chipster can also export data in a suitable format for uploading to the ArrayExpress [8] and GEO [9] databases.”
Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases (2018, methodology): “Network 4: GEO co-expression network The fourth network is a co-expression network based on Affymetrix HG-U133 Plus 2 arrays extracted from the Gene Expression Omnibus (GEO) (Barrett et al., 2011).”
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata (2011, neutral): “The NCBI and International Nucleotide Sequence Database Collaboration (INSDC) (1) archival databases hosting these data include GenBank (2), SRA (3), GEO (4), Epigenomics (5), dbSNP (6), dbVar (7) and dbGaP (8).”
ArrayExpress update—trends in database growth and links to data analysis tools (2012, methodology): “Approximately 20% of the data were submitted directly to ArrayExpress; the rest are imported from GEO weekly.”
The International Nucleotide Sequence Database Collaboration (2011, background): “Linkages may also be established between initiatives with data deposited in the INSDC sequence archives and repositories that house analysis of raw sequence output, such as GEO (4), ArrayExpress (5) and dbGaP.”
Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization (2012, methodology): “To this end, the gene expression series GSE2034, GSE7390 and GSE11121 were downloaded from the Gene Expression Omnibus (GEO) repository [20,21].”
ENCODE Data in the UCSC Genome Browser: year 5 update (2012, methodology): “ENCODE data now encompasses a total of 4835 GEO Samples and 98 GEO Series.”
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data (2016, methodology): “All our peak datasets were curated from NCBI GEO database (15), ENCODE project (16), modENCODE project (17,18) and NIH Roadmap Epigenomics Project (19) (Tables 1 and 2).”