Reactome: A Curated Pathway Database

Version 54 Released

Posted on October 1st, 2015, by Matthews, under Reactome Announcement, Reactome Release Announcement

In version V54, the topic Mitophagy has been added. New disease pathways include SLC transporter disorders, Essential pentosuria, Diseases associated with surfactant metabolism, Pentose phosphate pathway disease, and Glycogen storage diseases. Updated DNA repair pathways include Double-strand break repair, Nucleotide excision repair, and the Fanconi anemia pathway. Gene expression now covers tRNA processing and immune system annotations have been expanded to include MAP3K8 (TPL2)-dependent MAPK1/3 activation as well as updates to the Immunoregulatory interactions between a lymphoid and a non-lymphoid cell pathway. Under Metabolism, Surfactant metabolism and Catabolism of glucuronate to xylulose-5-phosphate have been added and Fructose metabolism has been revised. Metabolism of proteins includes additions to the Amyloid formation pathway. Signal transduction includes updates to the TNF signaling pathway and Vesicle-mediated transport now covers Cargo concentration in the ER as well as additions to COPII (Coat protein 2) mediated vesicle transport.

New pathway Illustrations are available for Asparagine N-linked glycosylation and DNA repair.

Alexander Barrow, James Borowiec, Stefan Bröer, Daniel ChaussKatie DeCicco-SkinnerMaria Fousteri, Kasper Fugger, Marc Kantorow, Louis Levinger, Yuri Motorin, and Harald Wajant are our external reviewers.  João Ribeiro  and José Carlos Cameselle have revised pathways for Reactome.

New Plant Reactome Website Released

Posted on August 31st, 2015, by robinhaw, under Reactome Announcement

Gramene is pleased to announce the release of the new Plant Reactome pathway database website at  This milestone is the highlight of Gramene release #47.  New Plant Reactome features include pathway analysis tools for researchers and an intuitive, menu-driven front page with quick links to the pathway browser, search features, and tutorials.  The analysis tools allow researchers to upload gene lists, Uniprot IDs, compound identifiers, and/or -omics expression studies to see their data displayed on the Plant Reactome pathway model along with a pathway enrichment analysis.  Inter-species pathway comparisons and advanced search features are also available.  The Plant Reactome is a database of plant metabolic and regulatory pathways, and currently provides over 200 manually curated Oryza sativa pathways, plus projections to 33 other plant species with
sequenced genomes and transcriptomes.

A complete description of the contents of this new release is available in our release notes (

Please let us know ( if you have questions or suggestions.

The Gramene Team

Version 53 Released

Posted on July 2nd, 2015, by robinhaw, under Reactome Announcement, Reactome Release Announcement

In version V53, signal transduction pathways have been updated to include mTOR signaling, MAPK6/MAPK4 signaling, the RAF/MAPK pathway and Deactivation of the beta-catenin transactivating complex.

New immune system pathway include the TNFRSF mediated non-canonical NF-kB pathway and Immunoregulatory interactions between Lymphoid and a non-Lymphoid cells.   

New disease pathways are Diseases associated with glycosylation precursor biosynthesis and ABC transporter diseases.

Other revised topics include Cellular responses to stress (Macroautophagy), Chromatin organization (HDMs demethylate histones) and developmental biology (LGI-ADAM interactions).

New pathway Illustrations are available for Cellular Senescence, Oncogene Induced Senescence, Oxidative Stress Induced Senescence, DNA Damage/Telomere Stress Induced Senescence, Senescence-Associated Secretory Phenotype (SASP).

Alexander Barrow, Sharon A Tooze, Vincent Harley, Richard Hopkinson, Simon Mathien, Dies Meijer, Sylvain Meloche, Ugo Moens, Karobi Moitra, Akhil Rajput, Robert Roskoski, Christopher Schofield, Ole-Morten Seternes, Mathilde Soulez, Dorothe Spillmann, David J Timson, Richard Virgen-Slane, Louise Walport, Carl F Ware, and Fried Zwartkruis are our external reviewers.

Version 52 Released

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


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.