Reactome: A Curated Pathway Database

Version 51 Release

Posted on December 9th, 2014, by robinhaw, under Reactome Announcement

As of version 51, Reactome has expanded its coverage of disease to new modules on the uptake and activity of tetanus and diphtheria toxins, Diseases associated with N-glycosylation of proteins, and Metabolic disorders of biological oxidation enzymes.  Also updated in this release are  Gene Expression (PIWI-interacting RNA (piRNA) biogenesis), Hemostasis (Formation of Fibrin Clot), Biological oxidations, Post-translational protein modification (Synthesis of diphthamide-EEF2), Organelle biogenesis and maintenance (Assembly of the primary cilium), Signal transduction (Signaling by Retinoic Acid and Hedgehog ‘on’ state), Gene expression, and Transmembrane transport of small molecules.

Katsiaryna BelayaGregg DuesterJoao GoncalvesShihui LiuYulu Cherry Liu, Esben Lorentzen, Andrew MumfordToshio Nakaki, Joseph Napoli, Kuniaki SaitoShashi  Sharma and Nagarajan Thirunavukkarasu are our external reviewers.

Reactome comprises 7,686 human reactions involving the 7,982 protein products of 7,760 human genes, and 1,428 small molecules. These reactions are organized into 1,597 pathways, supported by 17,939 PubMed literature references. We have projected these reactions onto 96,086 orthologous proteins, creating 20,804 orthologous pathways in 19 model organisms.

Reactome now provides linkouts to protein and small molecule annotations from the ZINC, a free database of commercially-available compounds for virtual screening.

After 10 years Reactome hits 50!

Posted on October 8th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

Reactome hits a major milestone: Reactome is now one of the largest freely accessible, open source pathway knowledgebases. Over the 10 years that Reactome has been curating and exporting pathway and reaction data, we’ve grown to include annotations for over 1/3 of the protein-coding genes in the current Ensembl human genome assembly. As of Version 50, Reactome comprises 7,642 human reactions involving the 7,597 protein products of 7,333 human genes, and 1,419 small molecules. These reactions are organized into 1,597 pathways, supported by 17,248 PubMed literature references. We have projected these reactions onto 99,812 orthologous proteins, creating 20,032 orthologous pathways in 19 model organisms.

New Pathways for this Release: Topics with revised content in V50 include Disease (Diseases associated with glycosaminoglycan metabolism), Gene expression (Transcriptional regulation by small RNAs and DNA methylation),  Organelle biogenesis and maintenance (Mitochondrial translation), Signal Transduction (Hedgehog ‘off’ state), Transmembrane transport of small molecules (Orphan transporters), and Metabolism. We’d like to thank Renee BeekmanCaiyong ChenZofia M Chrzanowska-LightowlersWolfgang FischleLong-Cheng LiYulu Cherry Liu, José I Martín-SuberoDavid S RosenblattDorothe SpillmannAnna Stroynowska-Czerwinska who are our external reviewers.

New Full-text Search Tool

Posted on July 24th, 2014, by robinhaw, under Reactome Announcement

Reactome is pleased to announce the release of a new search based upon the popular Apache Solr, which has full-text search capabilities, field searching, and provides ranked results and hit highlighting. This new search supports accurate and efficient querying of the Reactome knowledgebase, including protein, set, complex, chemical compound, reaction and pathway annotations. For those users that require more complex and logical queries, you can use the Lucene Query Syntax as described in the Advanced Search. Further details about the new search can be found in our User Guide.

Version 49 Released

Posted on July 15th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

In V49, Disease pathways have been expanded to include WNT in cancerUptake and function of anthrax toxins, and Processing-defective Hh variants abrogate ligand secretion. Metabolism now includes Aflatoxin activation and detoxification, and Immune system covers Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon. Development has been updated with EPH-EFN signaling. New pathways under signal transduction include Repression of Wnt target genesVEGFA-VEGFR2 signaling, and Hedgehog ligand biogenesis. Updated signal transduction modules include TCF dependent signaling in response to WNT and Degradation of beta-catenin by the destruction complex. Mismatch Repair has beed added to DNA repair and Chromatin organization has been expanded to cover HDACs deacetylate histonesRMTs methylate histone arginines, and HDMs demethylate histones. Akira Kikuchi is our external author. Kurt BallmerPhilipp BergerMichael EdelbrockErnesto GuccioneRichard HopkinsonNancy IpStephen LepplaShihui LiuYulu LiuAnna Maria MasciMahtab MoayeriNishani RajakulendranSima SalahshorChristopher SchofieldBenjamin E TurkLouise WalportMichael WelshJim Woodgett, and Xiang-Jiao Yang are our external reviewers.

New Reactome Pathway Analysis Portal Released

Posted on June 18th, 2014, by robinhaw, under Reactome Announcement, Reactome Feature

Pathway databases, like Reactome, are uniquely suited for interpreting the results of high-throughput functional genomics data sets such as microarray-based expression profiles, protein interaction sets, and chromatin IP. In response to user feedback and new feature requests, we have released a new Reactome Pathway Browser 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 is also available via RESTful web services. Further details about the new pathway analysis tool can be found in our User Guide.

Version 48 Released

Posted on March 27th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

New in V48 is Organelle biogenesis (Mitochondrial biogenesis). Topics with new or updated pathways include Cell cycle (Depolymerisation of the nuclear lamina), Cellular responses to stress (Cellular responses to heat stress, Development (Transcriptional regulation of pluripotent stem cells, Disease (Glycogen storage diseases (Myoclonic epilepsy of Lafora) and Neurotoxicity of clostridium toxins), Gene expression (Epigenetic regulation of gene expression), Metabolism of proteins (O-glycosylation of TSR domain-containing proteins and Sialic acid metabolism), and Signal transduction (TCF-dependent signaling in response to WNT. The Gallus gallus pathway Innate immune system has been updated to include Complement cascade. Luciano Di Croce, Matyas Gorjanacz, Ingrid Grummt, Angela M Lezza, Juan F Medrano, Mridul Mukherji, Bibhusita Pani, Bartholomew Pederson, Gerd Pfeifer, Nishani Rajakulendran, Yih-Horng Shiao, Renee van Amerongen, Renate Voit, Jianlong Wang, and Saumya Wickramasinghe are our external reviewers.

Version 47 Released

Posted on January 10th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

New in V47 is Chromatin organization (Chromatin modifying enzymes). Topics with new or revised events include Cellular response to stress (Cellular senescence and Detoxification of reactive oxygen species, Cell cycle (Condensation of prophase chromosomes), Immune system (Cell surface interaction at the vascular wall), Metabolism of proteins (Synthesis of dolichyl-phosphate), and Signal transduction (Beta-catenin independent WNT signaling). Brenda Gallie, is our external author. Tom KaragiannisMahendra KavdiaAkira KikuchiMichelle LongworthShamith Samarajiwa, and Jaap Jan Zwaginga are our external reviewers.

Reactome FI Cytoscape plugin: 4.0.0 beta Released

Posted on January 8th, 2014, by Marc Gillepsie, under Reactome Feature

We have released a new version of the Reactome FI Cytoscape plugin: 4.0.0 beta. This version provides a suite of features to help users to explore Reactome pathways directly in Cytoscape. Using these features, you can load pathways in the Reactome database into Cytoscape, visualize Reactome pathways in either the native pathway diagram view or the FI network view, do pathway enrichment analysis for a set of genes, and check genes from your list in identified  pathways.

Read more about the Reactome FI Cytoscape Plugin here.