Reactome: A Curated Pathway Database

Version 52 Released

Posted on March 23rd, 2015, by robinhaw, under Reactome Announcement, Reactome Release Announcement

Melanin_Biosynthesis

In version V52, Reactome has broadened its coverage of Disease to include Hereditary fructose intolerance, Essential fructosuria, Intestinal disaccharidase deficiencies, and Diseases associated with TLR signaling cascade.

New Metabolic pathways include Fructose biosynthesis, Lactose synthesis, and Melanin biosynthesis and Post-translational protein modification has been expanded to cover SUMOylation of DNA damage response and repair proteins.

The DNA repair pathways Base excision repair, DNA damage bypass, and DNA damage reversal have been revised and within Signal transduction, RHO GTPase Effectors is new and Deactivation of the beta-catenin transactivating complex has been updated.

New pathways have also been added to the topics of Gene Expression (TP53 regulates metabolic genes), Immune system (C-type lectin receptors (CLRs), Chromatin organization (PKMTs methylate histone lysines), and Programmed cell death (Regulated necrosis).

New pathway Illustrations are available for Circadian clock, DNA replication, DNA strand elongation, Immune system, Innate immune system, Membrane trafficking, Muscle contraction, and Visual phototransduction.

Francisco Rivero is our external author.

Mahdi Amiri, James Borowiec, Francis Ka-Ming Chan, Marco d’Ischia, Stefano Ferrari, Teunis Geijtenbeek, Paul Hwang, Shosuke Ito, Ju-Gyeong Kang, Douglas McDonald, Mo Motamedi, Hassan Naim, David Timson, Dean Tolan, Ping-Yuan Wang, and Aaron Zorn are our external reviewers.

Reactome comprises 8,169 human reactions involving the 8,183 protein products of 7,954 human genes, and 1,449 small molecules. These reactions are organized into 1,762 pathways, supported by 18,900 PubMed literature references. We have projected these reactions onto 98,602 orthologous proteins, creating 19,039 orthologous pathways in 18 model organisms.

New publications are online.

Posted on March 11th, 2015, by robinhaw, under Reactome Announcement, Reactome Publication

The Reactome tutorial paper entitled “Expression Data Analysis with Reactome” has been published in Current Protocols in Bioinformatics.  A second paper, “A visual review of the interactome of LRRK2: Using deep-curated molecular interactions data to represent biology“, which describes the use of IntAct data curation and Reactome pathway analysis tools to more accurately represent LRRK2-related knowledge has been published in Proteomics. More publications from the Reactome Team can be found here.

New miRBase-Reactome pathway identifier mapping files are available

Posted on February 9th, 2015, by robinhaw, under Reactome Feature

The set of identifier mapping files, linking different source database identifiers to the Reactome pathway diagram, has been updated to include a miRBase-pathway identifier mapping file. These mapping files consist of a tab-separated table that indicates which external protein (UniProt), gene (Ensembl), microRNA (miRBase) or small molecule (ChEBI) identifiers were mapped to Reactome pathway annotations. Our goal with distributing two sets of files for each different identifier type is to provide these mapping files link the source database identifier to: i) the lowest level pathway diagram or subset of the pathway, and ii) all level pathway diagrams. These mapping files are available from our Download Data page.

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 LiuEsben LorentzenAndrew MumfordToshio NakakiJoseph NapoliKuniaki 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.