Reactome: A Curated Pathway Database

Reactome celebrates release of 10,000th annotated protein

Posted on October 6th, 2016, by robinhaw, under Reactome Announcement, Reactome Release Announcement

10K_Reactome

The Reactome team is pleased to announce that it met a major milestone in October 2016 with the annotation and release of its 10,000th human protein. Reactome (www.reactome.org) is an open access curated knowledgebase which relates human genes, proteins and other biomolecules to the biological pathways and processes in which they participate. It is a key resource for the biomedical research community, and is widely used by researchers around the world to interpret high-throughput experiments in genetics, genomics and proteomics. Given that the human genome contains roughly 20,000 protein-coding genes in total, the annotation of the 10,000th protein means that Reactome now covers half of the protein-coding portion of the genome. This makes Reactome the most comprehensive open access pathway knowledgebase available to the scientific community.

By relating genes and proteins to normal and abnormal biological pathways, Reactome allows researchers to identify patterns in large data sets. For example, researchers can use Reactome to reduce an experiment that identified thousands of genes whose activities are altered in a disease to a manageable number of key biological pathways that are disrupted by these changes. Researchers can then combine Reactome with other databases to find drugs and protein targets that might reverse the pathway alterations, or to devise ways of diagnosing the disease at an early stage. Via its web site, online tools, and specialized visualization and analysis applications, Reactome has been incorporated into more than 400 third-party genome analysis tools, and has been cited more than 4,000 times in the scientific literature. 

Reactome has been in continuous operation since 2004 and is an international collaboration among the Ontario Institute for Cancer Research in Canada, New York University School of Medicine in the United States, and the European Bioinformatics Institute in the United Kingdom. It is staffed by expert biological curators, bioinformaticians and computer scientists. Much of its content is provided by community authors and peer reviewers who are assisted by the curatorial staff. The Reactome content, including pathway data and the software infrastructure, are available to all comers free of charge under a Creative Commons open access license. Reactome is supported by grants from the US National Institutes of Health, the Ontario Research Fund, the University of Toronto, OpenTargets, Genome Canada, and the European Molecular Biology Laboratory.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information please contact our helpdesk.

Version 58 Released

Posted on September 28th, 2016, by robinhaw, under Reactome Announcement, Reactome Release Announcement

illustration_deregulated_CDK5_triggers_multiple_neurodegenerative_pathways_72

New and Updated Pathways. With version V58, Reactome has annotations for over 10,000 human proteins. New or revised pathways include: Cell cycle (FBXL7 down-regulates AURKA during mitotic entry and in early mitosis), Developmental biology (Keratinization), Disease (Oncogenic MAPK signaling and Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models), Gene expression (PI5P Regulates TP53 Acetylation, Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors),  Immune system  (Neutrophil degranulation and Antimicrobial peptides), Metabolism of proteins (Synthesis of active ubiquitin: roles of E1 and E2 enzymes), Signal transduction (Signaling by MET and Downregulation of ERBB2 signaling), and Vesicle-mediated transport (RAB GEFs exchange GTP for GDP on RABs).

A pathway illustration is available for Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease .

Thanks to our Contributors. Our external author is Kavita Shah.  Emily Ayoub, Jorge Azevedo, Walter Birchmeier, Miroslav Blumenberg, Maria Bogachek, Nullin Divecha, Roman Dziarski, Rhys Grant, David Hains, Niels Heegard, Guustaaf Heynen, Catherine Lindon, Andrea Marat, Robert Stephens, Michel Tremblay, and Ronald Weigel are our external reviewers.

Reactome comprises 10,168 human reactions organized into 2,069 pathways involving 10,461 proteins encoded by 10,221 different human genes, and 1,710 small molecules. These annotations are supported by 24,974 literature references. We have projected these reactions onto 110,710 orthologous proteins, creating 19,991 orthologous pathways in 18 non-human species.

Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, New York University Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information please contact our helpdesk.

 

Version 57 Released

Posted on June 27th, 2016, by robinhaw, under Reactome Announcement, Reactome Release Announcement

In version V57, topics with new or revised pathways include: Developmental biology (RET signaling), Disease (Signaling by FGFR in disease and Defective CFTR causes cystic fibrosis), Gene expression (rRNA modification in the mitochondrion and Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors), Immune system (ER-Phagosome pathway, Interleukin-7 signaling, Regulation by endogenous TLR ligand, and TCR signaling), Metabolism (Lipid digestion, mobilization, and transport and Phosphate bond hydrolysis by NTPDase proteins). Metabolism of proteins (Deubiquitination), Neuronal system (Interactions of neurexins and neuroligins at synapses and SALM protein interactions at synapse). Signal transduction (EGFR downregulation, Signaling by FGFR1, and FGFRL1 modulation of FGFR1 signaling), Transmembrane transport of small molecules (ABC-family proteins mediated transport) and Vesicle-mediated transport (Clathrin-mediated endocytosis).

Our external author is Alba Sanchis. Costin AntonescuJohn Bergeron, Daniel BogenhagenNunzio BottiniGuang-Chao ChenIgor DawidRegina FluhrerNoriko GotohFrancesca GranucciRichard GrosePaul HeppenstallJing HuJan HuertasWenqin LuoMalay MandalBirgit MeldalDaniel MoralesTatsunori NishimuraRonald PetraliaGail SeaboldSunny SharmaStephanie StanfordJean SévignyPhilip WashbourneIvan Zanoni, and Valeria Zarelli are our external reviewers.

Version 56 Released

Posted on March 24th, 2016, by robinhaw, under Reactome Announcement, Reactome Release Announcement

Topics with new or revised content in V56 include Cell cycle (AURKA activation by TPX2, Interaction between PHLDA1 and AURKA, and The role of GTSE1 in G2/M progression after G2 checkpoint) , Disease (Diseases associated with O-glycosylation of proteins), Gene  expression (ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression, Major pathway of rRNA processing in the nucleus, RNA polymerase II transcribes snRNA genes, rRNA modification in the nucleus, and Transcriptional Regulation by TP53), Immune system (Signaling by Interleukins and related cytokines), Metabolism,  Metabolism of proteins (Cooperation of PDCL and TRiC/CCT in G-protein beta folding), Neuronal system (SALM protein interactions at synapse), and signal transduction (Amine ligand-binding receptors, Chemokine receptors bind chemokines, ERBB2 regulates cell motility, FGFR2 alternative splicing, G alpha (s) signaling events, PI5P, PP2A and IER3 regulate AKT signaling, and Signaling by PTK6).

Ali Badache, Alexander Bird, Helen Chen, Richard P Grose, Hiren J Joshi, Lars Hansen, Nouria Hernandez, Sebastian Iben, Alberto Inga, Eunjoon Kim, Erin J Adams, Adrienne Luoma, Christopher A Maxwell, Birgit Meldal,  Isabel Pires, Francoise Porteu, Robin Reed, Ana Rondon, Kavita Shah, Sunny Sharma, Nicholas G Vincent, Karen Vousden, Barry M Willardson, Stuart A Wilson, Sara Zaccara, and Dirk Zajonc  are our external reviewers. 

Version 55 Released

Posted on December 15th, 2015, by robinhaw, under Reactome Announcement, Reactome Release Announcement

In version V55, topics with new or revised pathways include: Developmental biology (Activation of anterior HOX genes in hindbrain development during early embryogenesis), Disease (ABC transporter diseases), Gene expression (B-WICH complex positively regulates rRNA expression and tRNA processing), Hemostasis (updated Cell surface interaction at the vascular wall and GPVI-mediated activation cascade), Immune system (IL-6 family signaling and Regulation of BCR signaling by CD22), Metabolism (Response to metal ions, Selenoamino acid synthesis and metabolism as well as updates to Complex I biogenesis and Metabolism of fat-soluble vitamins). Metabolism of proteins has been updated to include Protein repair as well as revisions to Amyloid fiber formation and SUMOylation. Cellular responses to stress includes an update to Macroautophagy, Muscle contraction has been expanded to include Cardiac conduction. Signal transduction includes updates to the RHO GTPases Activate NADPH Oxidases pathway, and Vesicle-mediated transport now covers COPI-mediated anterograde traffic.

Our external author is René Rezsohazy. Jan-Willem Akkerman, Sílvia Atrian, Angela Bachi, Francesco Blasi, Gianni Colotti, Giuseppe Filosa, David Fisher, Yaron Galanty, Nayef JarrousDaniel Klionsky,Taco Kuijpers, Rakesh Kumar, Birgit Meldal, Masashi Narazaki , James Paulson, Piergiorgio Percipalle, George Perry, Chris Powell, Mark Rush, Suneet Shukla, Guntram Suske, Tsutomu Suzuki, Toshio Tanaka, and Xiang-Dong Zhang are our external reviewers.

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.

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

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.

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.