doi: 10.1093/nar/gkn732. Epub 2008 Nov 7.
INTERFEROME: the database of interferon regulated genes
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- PMID:18996892
- PMCID: PMC2686605
- DOI: 10.1093/nar/gkn732
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INTERFEROME: the database of interferon regulated genes
Shamith A Samarajiwa et al. Nucleic Acids Res.2009 Jan.
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Abstract
INTERFEROME is an open access database of types I, II and III Interferon regulated genes (http://www.interferome.org) collected from analysing expression data sets of cells treated with IFNs. This database of interferon regulated genes integrates information from high-throughput experiments with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information to enable a detailed investigation of the molecular mechanisms underlying IFN biology. INTERFEROME fulfils a need in infection, immunity, development and cancer research by providing computational tools to assist in identifying interferon signatures in gene lists generated by high-throughput expression technologies, and their potential molecular and biological consequences.
Figures
The functionality of the INTERFEROME database is summarized in Figure 1, which displays some of the screen captures resulting from searching the database with a gene list. Its main functionality is the IRG signature page which identifies IRGs that were present in the gene list and displays associated annotation. In addition INTERFEROME's expression and promoter analysis capability is highlighted. An example search is demonstrated inSupplementary Figures .
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References
- Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD. How cells respond to interferons. Annu. Rev. Biochem. 1998;67:227–264. - PubMed
- Hertzog PJ, O’Neill LA, Hamilton JA. The interferon in TLR signaling: more than just antiviral. Trends Immunol. 2003;24:534–539. - PubMed
- Pestka S, Langer JA, Zoon KC, Samuel CE. Interferons and their actions. Annu. Rev. Biochem. 1987;56:727–777. - PubMed
- Schmidt KN, Ouyang W. Targeting interferon-alpha: a promising approach for systemic lupus erythematosus therapy. Lupus. 2004;13:348–352. - PubMed
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