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PMID: 23203888 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Interferome v2.0: an updated database of annotated interferon-regulated genes.

Nucleic acids research ·Vol. 41 ·No. Database issue ·2013-01-00 ·Pages D1040-6

Rusinova I, Forster S, Yu S, Kannan A, Masse M, Cumming H, Chapman R, Hertzog PJ

Abstract

Interferome v2.0 (http://interferome.its.monash.edu.au/interferome/) is an update of an earlier version of the Interferome DB published in the 2009 NAR database edition. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types I, II and III interferon (IFN)-treated cells, mice or humans. Quantitative, MIAME compliant data are collected, subjected to thorough, standardized, quantitative and statistical analyses and then significant changes in gene expression are uploaded. Comprehensive manual collection of metadata in v2.0 allows flexible, detailed search capacity including the parameters: range of -fold change, IFN type, concentration and time, and cell/tissue type. There is no limit to the number of genes that can be used to search the database in a single query. Secondary analysis such as gene ontology, regulatory factors, chromosomal location or tissue expression plots of IFN-regulated genes (IRGs) can be performed in Interferome v2.0, or data can be downloaded in convenient text formats compatible with common secondary analysis programs. Given the importance of IFN to innate immune responses in infectious, inflammatory diseases and cancer, this upgrade of the Interferome to version 2.0 will facilitate the identification of gene signatures of importance in the pathogenesis of these diseases.

MeSH Terms
Animals Databases, Genetic Gene Expression Regulation Humans Interferons/pharmacology Internet Mice Molecular Sequence Annotation Transcriptome
Chemicals
Interferons
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Rusinova Irina
Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
Forster Sam
Yu Simon
Kannan Anitha
Masse Marion
Cumming Helen
Chapman Ross
Hertzog Paul J
References (36)
36 references, click to expand
  1. Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape.
    Nat Med. 2012 Aug;18(8):1224-31 PMID: 22820642
  2. Type I interferon receptors: biochemistry and biological functions.
    J Biol Chem. 2007 Jul 13;282(28):20053-7 PMID: 17502368
  3. HIV infection of dendritic cells subverts the IFN induction pathway via IRF-1 and inhibits type 1 IFN production.
    Blood. 2011 Jul 14;118(2):298-308 PMID: 21411754
  4. Overview. Type I interferons as primers, activators and inhibitors of innate and adaptive immune responses.
    Immunol Cell Biol. 2012 May;90(5):471-3 PMID: 22648073
  5. Analysis of the cumulative changes in Graves' disease thyroid glands points to IFN signature, plasmacytoid DCs and alternatively activated macrophages as chronicity determining factors.
    J Autoimmun. 2011 May;36(3-4):189-200 PMID: 21354768
  6. [Immunizing property of vaccinia virus inactivated by ultraviolets rays].
    C R Seances Soc Biol Fil. 1954 Oct;148(19-20):1700-2 PMID: 14364998
  7. Patterns of pathogenesis: discrimination of pathogenic and nonpathogenic microbes by the innate immune system.
    Cell Host Microbe. 2009 Jul 23;6(1):10-21 PMID: 19616762
  8. Mechanisms of type-I- and type-II-interferon-mediated signalling.
    Nat Rev Immunol. 2005 May;5(5):375-86 PMID: 15864272
  9. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments.
    Bioinformatics. 2002 Apr;18(4):546-54 PMID: 12016052
  10. Functional role of type I and type II interferons in antiviral defense.
    Science. 1994 Jun 24;264(5167):1918-21 PMID: 8009221
  11. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
    Bioinformatics. 2003 Jan 22;19(2):185-93 PMID: 12538238
  12. Emerging therapies for systemic lupus erythematosus--focus on targeting interferon-alpha.
    Clin Immunol. 2012 Jun;143(3):210-21 PMID: 22525889
  13. Interferon-α for patients with chronic hepatitis delta: a systematic review of randomized clinical trials.
    Antivir Ther. 2012;17(6):1029-37 PMID: 22892440
  14. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
    Genome Biol. 2009;10(11):R130 PMID: 19919682
  15. IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy.
    Nat Genet. 2009 Oct;41(10):1100-4 PMID: 19749758
  16. Pattern recognition receptors and inflammation.
    Cell. 2010 Mar 19;140(6):805-20 PMID: 20303872
  17. Use of within-array replicate spots for assessing differential expression in microarray experiments.
    Bioinformatics. 2005 May 1;21(9):2067-75 PMID: 15657102
  18. Interferon-beta-1b-induced short- and long-term signatures of treatment activity in multiple sclerosis.
    Pharmacogenomics J. 2013 Oct;13(5):443-51 PMID: 22711062
  19. Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
    Biostatistics. 2003 Apr;4(2):249-64 PMID: 12925520
  20. Interferons, interferon-like cytokines, and their receptors.
    Immunol Rev. 2004 Dec;202:8-32 PMID: 15546383
  21. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis.
    Nature. 2010 Aug 19;466(7309):973-7 PMID: 20725040
  22. Summaries of Affymetrix GeneChip probe level data.
    Nucleic Acids Res. 2003 Feb 15;31(4):e15 PMID: 12582260
  23. The role of type I interferons in TLR responses.
    Immunol Cell Biol. 2007 Aug-Sep;85(6):446-57 PMID: 17667935
  24. Systems biology of interferon responses.
    J Interferon Cytokine Res. 2011 Jan;31(1):5-11 PMID: 21226606
  25. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  26. The JAK-STAT pathway at twenty.
    Immunity. 2012 Apr 20;36(4):503-14 PMID: 22520844
  27. Pregnant women have attenuated innate interferon responses to 2009 pandemic influenza A virus subtype H1N1.
    J Infect Dis. 2012 Sep 1;206(5):646-53 PMID: 22693225
  28. INTERFEROME: the database of interferon regulated genes.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D852-7 PMID: 18996892
  29. BASE--2nd generation software for microarray data management and analysis.
    BMC Bioinformatics. 2009 Oct 12;10:330 PMID: 19822003
  30. Direct effects of type I interferons on cells of the immune system.
    Clin Cancer Res. 2011 May 1;17(9):2619-27 PMID: 21372217
  31. Type I interferon: friend or foe?
    J Exp Med. 2010 Sep 27;207(10):2053-63 PMID: 20837696
  32. A null mutation in the gene encoding a type I interferon receptor component eliminates antiproliferative and antiviral responses to interferons alpha and beta and alters macrophage responses.
    Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):11284-8 PMID: 7479980
  33. Identification of genes differentially regulated by interferon alpha, beta, or gamma using oligonucleotide arrays.
    Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15623-8 PMID: 9861020
  34. Virus interference. I. The interferon.
    Proc R Soc Lond B Biol Sci. 1957 Sep 12;147(927):258-67 PMID: 13465720
  35. Cancer immunotherapy: the interferon-alpha experience.
    Semin Oncol. 2002 Jun;29(3 Suppl 7):18-26 PMID: 12068384
  36. Normalization of cDNA microarray data.
    Methods. 2003 Dec;31(4):265-73 PMID: 14597310
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks1215
Published
2013-01-00
Epub
2012-00-29
Pages
D1040-6
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3531205
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gks1215 PMC Full Text View journal details
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