GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest.

Database : the Journal of Biological Databases and Curation
Constance M SmithMartin Ringwald

Abstract

The Gene Expression Database (GXD), an extensive community resource of curated expression information for the mouse, has developed an RNA-Seq and Microarray Experiment Search (http://www.informatics.jax.org/gxd/htexp_index). This tool allows users to quickly and reliably find specific experiments in ArrayExpress and the Gene Expression Omnibus (GEO) that study endogenous gene expression in wild-type and mutant mice. Standardized metadata annotations, curated by GXD, allow users to specify the anatomical structure, developmental stage, mutated gene, strain and sex of samples of interest, as well as the study type and key parameters of the experiment. These searches, powered by controlled vocabularies and ontologies, can be combined with free text searching of experiment titles and descriptions. Search result summaries include link-outs to ArrayExpress and GEO, providing easy access to the expression data itself. Links to the PubMed entries for accompanying publications are also included. More information about this tool and GXD can be found at the GXD home page (http://www.informatics.jax.org/expression.shtml). Database URL: http://www.informatics.jax.org/expression.shtml.

References

Feb 8, 2005·Genome Biology·Jonathan BardMichael Ashburner
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Aug 27, 2013·Journal of Biomedical Semantics·Terry F HayamizuRichard A Baldock
May 6, 2015·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Constance M SmithMartin Ringwald
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Oct 20, 2018·Nucleic Acids Research·Constance M SmithMartin Ringwald
Oct 26, 2018·Nucleic Acids Research·Awais AtharAlvis Brazma

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Citations

Oct 27, 2020·Nucleic Acids Research·Richard M BaldarelliMartin Ringwald
Oct 27, 2021·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Martin RingwaldCarol J Bult

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Datasets Mentioned

BETA
GXD

Methods Mentioned

BETA
RNA-seq
transcription profiling
transgenic

Software Mentioned

ArrayExpress
Theiler
learn
GXD
MINSEQE
scikit
Transcriptomine

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