NCBI GEO: archive for high-throughput functional genomic data

By Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, D. Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, K. A. Marshall and 4 more. Nucleic Acids Res., 2008

1,083 citations recorded by the source corpus.

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e1b3fd0c124214a672f6642458a873462168963d

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Citations in the corpus

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-”
Molecular signatures database (MSigDB) 3.0 (2011, background): “0 include links to source datasets in Gene Expression Omnibus (GEO) (Barrett, 2009) and ArrayExpress (Parkinson, 2009).”
The case for cloud computing in genome informatics (2010, methodology): “Sequencing labs submit their data to big archival databases such as GenBank at the National Center for Biotechnology Information (NCBI) [1], the European Bioinformatics Institute EMBL database [2], DNA Data Bank of Japan (DDBJ) [3], the Short Read Archive (SRA) [4], the Gene Expression Omnibus (GEO)”
NCBI GEO: archive for functional genomics data sets—10 years on (2010, background): “The overarching design and organization of GEO remains largely unchanged from previous descriptions (5).”
MicrobesOnline: an integrated portal for comparative and functional genomics (2009, methodology): “MicrobesOnline contains only a partial import of the GEO database, but this will be expanded in future updates to MicrobesOnline.”
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data (2010, methodology): “Twenty-one Ago or TNRC6 CLIP-Seq sequence data sets and 10 Degradome-Seq sequence data sets were compiled from eight related studies (20–27) and downloaded from NCBI GEO database (28) or obtained from the Supplementary Data of the original articles (20–27).”
The Influence of Feature Selection Methods on Accuracy, Stability and Interpretability of Molecular Signatures (2011, neutral): “breast cancer datasets from Gene Expression Omnibus”
Cistrome: an integrative platform for transcriptional regulation studies (2011, neutral): “Currently, databases such as the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [33] and the European Bioinformatics Institute (EBI) ArrayExpress [34] host array data, and databases such as the NCBI Sequence Reads Archive (SRA) [35] and the EBI SRA host…”
Database resources of the National Center for Biotechnology Information (2009, background): “The BLAST programs (12–14) perform sequencesimilarity searches against a variety of nucleotide and protein databases, returning a set of gapped alignments with links to full sequence records as well as to related transcript clusters (UniGene), annotated gene loci (Gene), 3D structures [Molecular Mod”
The International Nucleotide Sequence Database Collaboration (2010, methodology): “The strategy adopted by INSDC has been the establishment of close collaborations with groups having specialized expertise, such as GEO (6) and ArrayExpress (7) for functional genomics experiments.”
NCBI GEO: archive for functional genomics data sets—update (2012, methodology): “Much of the infrastructure, organization and search capabilities of GEO remain as previously described (9), but several recent enhancements offer the user alternative Figure 1.”
Database resources of the National Center for Biotechnology Information (2010, background): “Gene Expression Omnibus (GEO) (25) is a data repository and retrieval system for high-throughput functional genomic data generated by microarray and nextgeneration sequencing technologies.”