Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

By Ron Edgar, Michael Domrachev, A. Lash. Nucleic Acids Res., 2002

12,718 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/1037548f688bd3e566df0d4184509976695124cf

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Citations in the corpus

Database resources of the National Center for Biotechnology (2003, background): “The GEO (22) is a data repository and retrieval system for gene expression data derived from any organism or artificial source.”
The Application of Deep Learning in Cancer Prognosis Prediction (2020, background): “The Gene Expression Omnibus (GEO) database is a public data repository storing microarray and next-generation sequencing (NGS) data, as well as other high-throughput functional genomic datasets, such as genome methylation, chromatin structure, genomic mutation/copy number variation, protein profilin”
Gene expression profiling of the tumor microenvironment during breast cancer progression (2009, methodology): “The data discussed in this publication have been deposited in the NCBI Gene Expression Omnibus [16] and are accessible [GEO:GSE14548] [17].”
9) TM4 Microarray Software Suite (2006, background): “Two popular microarray data repositories are ArrayExpress (Brazma et al., 2003, 2006) and Gene Expression Omnibus (GEO; Barrett and Edgar, 2006; Edgar et al., 2002).”
Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. (2015, methodology): “A central depository for plant imaging data, such as GEO [40,41] for sequencing data, is critical for easily aggregating and accessing imaging data.”
Data integration in the era of omics: current and future challenges (2014, methodology): “An example is the Gene Expression Ombinus (GEO [8,9]); GEO (similarly to ArrayExpress [23]) is a data repository for microarray and NGS data that requires the data producers to submit data following the Minimum Information About a Microarray Experiment (MIAME) guidelines [24].”
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains (2007, background): “While there are reports of both a larger, less abundant transcript and of a much smaller trophoblast specific transcript (TncRNA) that map to the human NEAT1 locus [28,29,31], both of these transcripts lie outside any region of conservation.”
High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation[C][W][OA] (2011, methodology): “The microarray data used in this article have been deposited in NCBI’s Gene Expression Omnibus (Edgar et al., 2002) and have been given a GEO Series accession number, GSE22982.”
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis (2010, methodology): “tuberculosis) obtained from the Many Microbes Database (39) and Gene Expression Omnibus (40).”
Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures (2010, methodology): “Gene-expression information from microarray data repositories such as Gene-expression Omnibus (19) and ArrayExpress (53) as well as from more specialized resources such as the drug response profile database Cmap (10) can be readily converted to ranked list inputs for our program.”
The digestive system is a potential route of 2019-nCov infection: a bioinformatics analysis based on single-cell transcriptomes (2020, neutral): “gov/)[12], Single Cell Portal 1 (https://singlecell.”
Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network (2011, methodology): “0 microarray data sets were obtained from the Gene Expression Omnibus (GEO) database (25).”
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data (2003, methodology): “Expression data for the three different microarray experiments is available at Gene Expression Omnibu”
A MicroRNA Superfamily Regulates Nucleotide Binding Site–Leucine-Rich Repeats and Other mRNAs[W][OA] (2012, methodology): “Analysis of abundance of miR482/2118 superfamily was performed through miRProf analysis of published large-scale data sets derived from various plant species available through the Gene Expression Omnibus (GEO) platform (Edgar et al., 2002).”
The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation (2010, methodology): “The AS microarray data have been deposited in NCBI’s Gene Expression Omnibus (Edgar et al., 2002) and are accessible through GEO series accession number GSE22963 (http://www.ncbi.nlm.nih.gov/geo/query/acc. cgi?acc=GSE22963).”
NCBI GEO: mining tens of millions of expression profiles—database and tools update (2006, methodology): “The overall structure of the core GEO database remains as described previously (1,2).”