Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
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TLDR
The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.Abstract:
The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.read more
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Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
NCBI GEO: archive for functional genomics data sets—update
Tanya Barrett,Stephen E. Wilhite,Pierre Ledoux,Carlos Evangelista,Irene F. Kim,Maxim Tomashevsky,Kimberly A. Marshall,Katherine Phillippy,Patti M. Sherman,Michelle Holko,Andrey Yefanov,Hye Seung Lee,Naigong Zhang,Cynthia L. Robertson,Nadezhda Serova,Sean Davis,Alexandra Soboleva +16 more
TL;DR: The Gene Expression Omnibus is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community and supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable.
Journal ArticleDOI
Inferring tumour purity and stromal and immune cell admixture from expression data
Kosuke Yoshihara,Maria Shahmoradgoli,Emmanuel Martinez,Rahulsimham Vegesna,Hoon Kim,Wandaliz Torres-Garcia,Victor Trevino,Hui Shen,Peter W. Laird,Douglas A. Levine,Scott L. Carter,Gad Getz,Katherine Stemke-Hale,Gordon B. Mills,Roel G.W. Verhaak +14 more
TL;DR: A method that uses gene expression signatures to infer the fraction of stromal and immune cells in tumour samples and prediction accuracy is corroborated using 3,809 transcriptional profiles available elsewhere in the public domain.
Journal ArticleDOI
A gene atlas of the mouse and human protein-encoding transcriptomes
Andrew I. Su,Tim Wiltshire,Serge Batalov,Hilmar Lapp,Keith A. Ching,David Block,Jie Zhang,Richard Soden,Mimi Hayakawa,Gabriel Kreiman,Gabriel Kreiman,Michael P. Cooke,John R. Walker,John B. Hogenesch,John B. Hogenesch +14 more
TL;DR: In this paper, high-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale, and the authors have designed custom arrays that interrogate the expression of the vast majority of proteinencoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues.
Journal ArticleDOI
GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox
TL;DR: Genevestigator as mentioned in this paper is a web-browser interface for gene expression analysis using Affymetrix GeneChip data, which allows users to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs.
References
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Journal ArticleDOI
Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
TL;DR: A high-capacity system was developed to monitor the expression of many genes in parallel by means of simultaneous, two-color fluorescence hybridization, which enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA.
PatentDOI
Serial analysis of gene expression
Kenneth W. Kinzler,Victor Velculescu,Bert Vogelstein,Lin Zhang,ヴェルヴレスク,ヴィクター,イー.,ヴォゲルステイン,バート,キンズラー,ケネス,ダブリュ.,ツァン,リン +7 more
TL;DR: Serial analysis of gene expression (SAGE) should provide a broadly applicable means for the quantitative cataloging and comparison of expressed genes in a variety of normal, developmental, and disease states.
Journal Article
Serial analysis of gene expression
TL;DR: Serial analysis of gene expression (SAGE) is a sequenced-based technique, which permits comprehensive and quantitative gene expression profiles from specific tissues or cells, which has been successfully applied for transcriptome research and identification of differentially expressed genes between mRNA populations.
Book ChapterDOI
Using oligonucleotide probe arrays to access genetic diversity
Robert J. Lipshutz,Don Morris,Mark S. Chee,Earl Hubbell,Michael J. Kozal,Nila Shah,N. Shen,Ruigang Yang,Stephen P. A. Fodor +8 more
TL;DR: Results from this application strongly suggest that oligonucleotide probe arrays will be a powerful tool for rapid investigations in sequence checking, pathogen detection, expression monitoring and DNA molecular recognition.
Journal ArticleDOI
Gene expression informatics--it's all in your mine.
TL;DR: Improved access to large electronic data sets, reliable and consistent annotation and effective tools for 'data mining' are critical to realize the full potential of whole–genome RNA expression studies.
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