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[Gofriends] [Reactome-announce] Version 35 of the Reactome Knowledgebase has been released

Robin Haw Robin.Haw at oicr.on.ca
Tue Dec 21 10:06:34 PST 2010


Version 35 includes the new topic Circadian clock<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_24941.1>. New and revised pathways include four in the immune system signaling module (Interferon signaling<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_25229.1>, RIG-I/MDA5 mediated induction of IFN alpha/beta<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_25359.1>, Advanced Glycosylation End product Receptor signaling<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_25195.1>, and Toll like Receptor Cascades<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6966.5>), Interactions of the DSCAM immunoglobulin superfamily proteins<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25299.1>, GABA receptor activation in synaptic transmission<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25199.1>, Regulation of mRNA stability by AU-rich elements<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24994.1>, Vitamin B1 metabolism <http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11117.1> and Molybdenum cofactors biosynthesis<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=%20REACT_25073.1>, Vitamin A uptake in enterocytes<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24968.1>, Transport of glycoproteins to the Golgi<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25046.1>, and in our project to catalog transport processes systematically, Iron uptake and transport<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25060.1> and Ion channel transport<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25300.1>. G Dall’Olio<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Dall'Olio+G%5BAuthor%5D> and R Stephan<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Stephan+R%5BAuthor%5D> are our external authors in this release. U Albrecht<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Albrecht+U%5BAuthor%5D>, S Akira<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Akira+S%5BAuthor%5D>, J Clemens<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Clemens+J%5BAuthor%5D>, F Delaunay<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Delaunay+F%5BAuthor%5D>, P Gagneux<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Gagneux+P%5BAuthor%5D>, L He<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=He+L%5BAuthor%5D>, T Kawai<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Kawai+T%5BAuthor%5D>, S Kay<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Kay+S%5BAuthor%5D>, S Restituito<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Restituito+S%5BAuthor%5D>, AA Sater<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Sater+AA%5BAuthor%5D>, C Schindler<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Schindler+C%5BAuthor%5D>, H Tsuyoshi<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Tsuyoshi+H%5BAuthor%5D>, J Wilusz<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Wilusz+J%5BAuthor%5D>, and SD Yan <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=DetailsSearch&Term=Yan+SD%5BAuthor%5D> are our external reviewers.

A new feature for the Reactome website is “Pathway of the Month” which highlights a particular pathway from Reactome. This month’s pathway is Influenza Infection<http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6167.3>.

The Reactome FI Cytoscape<http://www.cytoscape.org/> Plugin provides access to the Reactome Functional Interaction (FI) Network, a set of protein-protein interaction pairs scored by quality that links proteins curated in Reactome to other human proteins and covers close to 50% of human proteins (Wu et al. 2010<http://genomebiology.com/content/11/5/R53>). This plugin is useful in the discovery of network patterns related to cancer and other types of disease. The Reactome FI plugin is available for download<http://chianti.ucsd.edu/cyto_web/plugins/> (search term: Reactome FI) and the user guide is accessible here<http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin>.

Reactome will appear in the annual Database Issue of Nucleic Acids Research (Croft et al. 2011<http://nar.oxfordjournals.org/content/early/2010/11/23/nar.gkq1018.long>). This article has been chosen by the Editors of Nucleic Acids Research to appear on their Featured Articles<http://www.oxfordjournals.org/our_journals/nar/featured_articles.html> page. Featured Articles represent the top 5% of NAR papers in terms of originality, significance and scientific excellence.

A full description of the new and updated pathways available on the Reactome website at http://www.reactome.org<http://www.reactome.org/>.

Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center, and The European Bioinformatics Institute. Freely available to everyone worldwide, the Reactome database offers pathway data encapsulating areas of human biology ranging from metabolism to complex events such as GPCR signaling and apoptosis, extracted from the published literature by Reactome curatorial staff and cross-referenced to a wide range of standard biological databases. Reactome data and software are distributed under the terms of the Creative Commons Attribution 3.0 Unported License.

For more information contact:
Robin Haw
Email: help at reactome.org<mailto:help at reactome.org>
Tel: 647-260-7985

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