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Nucleic Acids Res. 2011 Jan;39(Database issue):D1011-5. doi: 10.1093/nar/gkq1259.

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.

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  • 1Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA.

Abstract

Various databases have harnessed the wealth of publicly available microarray data to address biological questions ranging from across-tissue differential expression to homologous gene expression. Despite their practical value, these databases rely on relative measures of expression and are unable to address the most fundamental question--which genes are expressed in a given cell type. The Gene Expression Barcode is the first database to provide reliable absolute measures of expression for most annotated genes for 131 human and 89 mouse tissue types, including diseased tissue. This is made possible by a novel algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results in a matter of seconds. The raw data, curated annotation, and code used to create our resource are also available at http://rafalab.jhsph.edu/barcode.

PMID:
21177656
[PubMed - indexed for MEDLINE]
PMCID:
PMC3013751
Free PMC Article

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