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[go-friends] Reactome Announcement: Version 49 of Reactome Knowledgebase has been released.

Robin Haw Robin.Haw at oicr.on.ca
Mon Jul 21 21:13:33 PDT 2014


[Print]<http://www.reactome.org>
[Hhg]<http://www.reactome.org/PathwayBrowser/#DIAGRAM=5358346&PATH=162582,5358351>

New for Release 49: Disease pathways have been expanded to include WNT in cancer<http://www.reactome.org/PathwayBrowser/#REACT_228331>, Uptake and function of anthrax toxins<http://www.reactome.org/PathwayBrowser/#REACT_228255>, and Processing-defective Hh variants abrogate ligand secretion<http://www.reactome.org/PathwayBrowser/#REACT_228190>. Metabolism now includes Aflatoxin activation and detoxification<http://www.reactome.org/PathwayBrowser/#REACT_228214>, and Immune system covers Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon<http://www.reactome.org/PathwayBrowser/#REACT_25148>. Development has been updated with EPH-EFN signaling<http://www.reactome.org/PathwayBrowser/#REACT_228170>. New pathways under Signal Transduction include TCF-dependent signaling in response to WNT<http://www.reactome.org/PathwayBrowser/#REACT_200777>, VEGFA-VEGFR2 signaling<http://www.reactome.org/PathwayBrowser/#REACT_228166>, and Hedgehog ligand biogenesis<http://www.reactome.org/PathwayBrowser/#REACT_228134>. Mismatch Repair<http://www.reactome.org/PathwayBrowser/#REACT_228013> has been added to DNA repair, and Chromatin Organization has been expanded to cover HDACs deacetylate histones<http://www.reactome.org/PathwayBrowser/#REACT_228222>, RMTs methylate histone arginines<http://www.reactome.org/PathwayBrowser/#REACT_228108>, and HDMs demethylate histones<http://www.reactome.org/PathwayBrowser/#REACT_228178>. We’d like to thank our external contributors. Akira Kikuchi<http://www.ncbi.nlm.nih.gov/pubmed?term=Kikuchi%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24562386> is our external author. Kurt Ballmer<http://www.psi.ch/lbr/ballmer_-kurt>, Philipp Berger<http://www.ncbi.nlm.nih.gov/pubmed/?term=Philipp+Berger>, Michael Edelbrock<http://www.ncbi.nlm.nih.gov/pubmed?term=Michael%20A%20Edelbrock%5BAuthor%5D>, Ernesto Guccione<http://www.imcb.a-star.edu.sg/php/eg.php>, Richard Hopkinson<http://www.ncbi.nlm.nih.gov/pubmed?term=Richard%20Hopkinson>, Nancy Ip<http://www.ncbi.nlm.nih.gov/pubmed?term=Nancy%20Y%20Ip%5BAuthor%5D>, Stephen Leppla<http://www.ncbi.nlm.nih.gov/pubmed?term=Stephen%20H%20Leppla%5BAuthor%5D>, Shihui Liu<http://www.ncbi.nlm.nih.gov/pubmed?term=Shihui%20Liu%5BAuthor%5D>, Yulu Liu<http://www.ncbi.nlm.nih.gov/pubmed?term=Liu%20YC%5BAuthor%5D&cauthor=true&cauthor_uid=22319451>, Anna Maria Masci<http://www.ncbi.nlm.nih.gov/pubmed?term=Masci%20AM%5BAuthor%5D&cauthor=true&cauthor_uid=23326591>, Mahtab Moayeri<http://www.ncbi.nlm.nih.gov/pubmed?term=Mahtab%20Moayeri%5BAuthor%5D>, Nishani Rajakulendran<http://www.ncbi.nlm.nih.gov/pubmed?term=Nishani%20Rajakulendran%5BAuthor%5D>, Sima Salahshor<http://www.salahshor.com/>, Christopher Schofield<http://www.ncbi.nlm.nih.gov/pubmed?term=Schofield%20CJ%5BAuthor%5D&cauthor=true&cauthor_uid=24859458>, Benjamin E Turk<http://www.yale.edu/turklab/>, Louise Walport<http://www.ncbi.nlm.nih.gov/pubmed?term=Louise%20Walport%5BAuthor%5D>, Michael Welsh<http://www.mcb.uu.se/res/groups/mw/>, Jim Woodgett<http://www.ncbi.nlm.nih.gov/pubmed?term=Woodgett%20J%5BAuthor%5D&cauthor=true&cauthor_uid=22665058>, and Xiang-Jiao Yang <http://www.ncbi.nlm.nih.gov/pubmed?term=Yang%20XJ%5BAuthor%5D&cauthor=true&cauthor_uid=23393134> are our external reviewers.

New Reactome Pathway Analysis Portal: In response to user feedback and new feature requests, we have released a new Reactome Pathway Browser<http://www.reactome.org/PathwayBrowser/> with an integrated suite of tools for pathway analysis. Using these improved features, you can map protein lists to Reactome pathways, perform pathway overrepresentation analysis for a set of genes, colourize pathway diagrams with gene expression data, and compare model organism and human pathways. To support third-party tool integration, the Reactome Pathway Analysis Portal<http://www.reactome.org/PathwayBrowser/#TOOL=AT> is also available via RESTful web services. Further details about the new pathway analysis tool can be found in our User Guide<http://wiki.reactome.org/index.php/Usersguide>.

Feature Update - Molecules tab in the Pathway Browser: The Molecules tab in the Pathway Browser<http://www.reactome.org/PathwayBrowser/> now has improved interactivity and usability, allowing users to easily list or download all molecule information from the currently displayed Pathway Diagram.

New Reactome Publications: Two new Reactome papers entitled “A controlled vocabulary for pathway entities and events<http://database.oxfordjournals.org/content/2014/bau060.full?keytype=ref&ijkey=5vukyCbDLpzKSa2>” and “ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis<http://f1000research.com/articles/3-146/>” have been published in DATABASE<http://database.oxfordjournals.org/> and F1000Research<http://f1000research.com/>, respectively. More publications from the Reactome Team<http://www.reactome.org/?page_id=581> can be found here<http://www.reactome.org/?page_id=1001>.

Important Dates:  Members of the Reactome Team<http://www.reactome.org/?page_id=581> will be attending the FEBS-EMBO 2014<http://www.febs-embo2014.org> Meeting in Paris, France from 30 August – 4 September, and the ECCB’14<http://www.eccb14.org> Meeting in Strasbourg, France from 7-10 September.

Follow us on Twitter: @reactome<https://twitter.com/reactome> to get frequent updates about new and updated pathways, feature updates, and more!

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.Reactome data and software are distributed under the terms of the Creative Commons Attribution 3.0 Unported License. A full description of the new and updated content is available on the Reactome website<http://www.reactome.org>.

For more information, contact: Robin Haw, help [at] reactome.org<http://reactome.org>.
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