Open Access News

News from the open access movement

Tuesday, October 02, 2007

An OA database of transcriptomic and proteomic data

A. Hijikata and 39 co-authors, Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells, Bioinformatics, September 25, 2007.  I'm linking to the PubMed abstract because the relevant issue of the journal isn't yet online.

Motivation:  Although a huge amount of mammalian genomic data does become publicly available, there are still hurdles for biologists to overcome before such data can be fully exploited. One of the challenges for gaining biological insight from genomic data has been the inability to cross-reference transcriptomic and proteomic data using a single informational platform. To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells. RESULTS: The database, named RefDIC (Reference genomics Database of Immune Cells), currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry; and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells. RefDIC is the first open-access database for immunogenomics and serves as an important information-sharing platform, enabling a focused genomic approach in immunology.

Availability:  All raw data and information can be accessed from [the RCAI RefDIC]. The microarray data is also available at [CIBEX] under CIBEX accession no. CBX19, and [PRIDE] under PRIDE accession nos. 2354 to 2378 and 2414.

Update. Rufus Pollock points out that this database does not permit commercial re-use.