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- Title
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.
- Authors
McCall, Matthew N; Uppal, Karan; Jaffee, Harris A; Zilliox, Michael J; Irizarry, Rafael A
- 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.
- Publication
Nucleic acids research, 2011, Vol 39, Issue Database issue, pD1011
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gkq1259