Reactome: A Curated Pathway Database
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IT IS NOT STABLE, IS LINKED TO AN INCOMPLETE DATA SET, AND IS NOT MONITORED FOR PERFORMANCE. WE STRONGLY RECOMMEND THE USE OF OUR PUBLIC SITE

Version 61 Released

Posted on August 1st, 2017, by robinhaw, under Reactome Announcement

In version V61, topics with new or revised pathways include: Gene expression (Transcriptional regulation by RUNX1), Immune System (Interleukin-12 family signaling), Signal Transduction (PTEN Regulation), and Transport of small molecules (Intracellular oxygen transport).

Arkaitz Carracedo and Leonardo Salmena were our external authors.

Sabine Bailly, Thorsten Burmester, Linda Shyue Huey Chuang, Yoshiaki Ito, Nisha KriplaniNick Leslie, and Esther van de Vosse were our external reviewers.

Annotation Statistics. Reactome comprises 11,042 human reactions organized into 2,148 pathways involving 10,940 proteins encoded by 10,691 different human genes, 1,763 small molecules, and 11,041 complexes. These annotations are supported by 26,859 literature references. We have projected these reactions onto 120,804 orthologous proteins, creating 20,780 orthologous pathways in 18 non-human species. Version 61 has annotations for 1,334 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 906 disease-specific reactions organized into 453 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Oregon Health and Science University, New York University Langone 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 60 Released

Posted on August 1st, 2017, by robinhaw, under Reactome Announcement, Reactome Release Announcement

New and Updated Pathways. In version V60, topics with new or revised pathways include: Cell cycle (Cyclin D associated events in G1), Cell-cell communication (SDK interactions), Cellular response to external stimuli (HSP90 chaperone cycle for steroid hormone receptors (SHR)), Disease (Diseases of Mismatch Repair), Gene Expression (TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest and Transcriptional Regulation by the CBFB:RUNX3 complex), Immune System (Butyrophilins and Regulation of complement cascade), Metabolism (Synthesis of IP2, IP, and Ins in the cytosol, Synthesis of PIPs at the early endosome membrane, Synthesis of PIPs at the ER membrane, Synthesis of PIPs at the late endosome membrane, and Synthesis of PIPs at the plasma membrane), Metabolism of proteins (CREB3 factors activate genes, Neddylation, Protein ubiquitination, and SUMOylation of chromatin organizing proteins), Mitophagy (Receptor Mediated Mitophagy), Neuronal System (Receptor protein tyrosine phosphatases interactions), Organelle biogenesis and maintenance (Cristae formation), and Transport of small molecules (Mitochondrial calcium ion transport).

Thanks to our Contributors.  Wei-Chih Yang and Jian Lu are our external  authors. Joseph Ainscough, Sanjeevani  Arora, Jorge E Azevedo,  Jeehyeon Bae, Lucia Banci, Gautam Bhave, David R Brown, Roberta Bulla, Alexandre M Carmo, Linda Shyue Huey Chuang, Karlene A Cimprich, Laura Crisponi, Alain de Bruin, Luisa Di Stefano , Ilaria Drago, Pablo C Echeverria, Du Feng, Emer S Ferro, Dianne Ford, Frances V Fuller-PaceCem Gabay, Dominique Gagliardi, Marcia  Haigis, J Wade Harper, Barry Honig, Yoshiaki Ito, Veerle Janssens, Nathalie Josso, Jaewon  Ko , Vera Kozjak-PavlovicAnastasia Kralli, Paul J Lehner, Dominique  Leprince, Bruce D Levy, Wei Li, Francisco Lozano, Jian Lu, Michael J Matunis, Birgit Meldal, Violaine Moreau, Kyungjae Myung, Joseph H Neale, Christian Obinger,  R Jeroen Pasterkamp, Richard Phipps, Didier Picard, Elah Pick, David A Rhodes, Pier e P Roger, Mark G Rush, Joshua R Sanes, Martin Schröder, Pierre Thibault, Dick J H van den Boomen , Thomas E Van Dyke, Roberto M Vanacore, Nobutaka Wakamiya, Qinglu Wang, Bart Westendorp, Sandra E Wiley, Miriam Wittmann, Guilherme Xavier, Wei-Chih Yang, Ali A Zarrin, and Bing Zhu are our external reviewers.

Annotation Statistics. Reactome comprises 10,754 human reactions organized into 2,132 pathways involving 10,907 proteins encoded by 10,658 different human genes, 1,763 small molecules, and 10,748 complexes. These annotations are supported by 26,384 literature references. We have projected these reactions onto 115,881 orthologous proteins, creating 20,701 orthologous pathways in 18 non-human species. Version 60 has annotations for 1,503 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 906 disease-specific reactions organized into 453 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Oregon Health and Science University, New York University Langone 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 59 Released

Posted on January 15th, 2017, by robinhaw, under Reactome Announcement, Reactome Release Announcement

New and Updated Pathways. In version V59, topics with new or revised pathways include: Disease (Listeria monocytogenes entry into host cells), Hemostasis (Cell surface interaction at the vascular wall), Immune System (Butyrophilins, Interleukin 10 signalling, and Interleukin-4 and 13 signaling), Metabolism (Nicotinate metabolism, Synthesis of PIPs at the nuclear envelope, Vitamin B5 (pantothenate) metabolism, and Aryl hydrocarbon receptor signalling), Metabolism of proteins (E3 ubiquitin ligases ubiquitinate target proteins, Peptide-ligand binding receptors, Protein methylation, RAB geranylgeranylation), Signal transduction (Class A/1 (Rhodopsin-like receptors), and Vesicle-mediated transport (TBC RABGAPs).

Thanks to our Contributors. Our external reviewers are Jorge Azevedo, Ester BoixLu DengPål Falnes, Vardan Karamyan, Samuel Leibovich, Weei-Chin LinCharuta Palsuledesai, Joel Pomerantz, Walter Reith, Sylvie Ricard-Blum, Christian Schwerk, Bruce Spiegelman, and Xiaochun Yu.

Annotation Statistics. Reactome comprises 10,391 human reactions organized into 2,080 pathways involving 10,624 proteins encoded by 10,381 different human genes, and 1,735 small molecules. These annotations are supported by 25,449 literature references. We have projected these reactions onto 115,881 orthologous proteins, creating 20,164 orthologous pathways in 18 non-human species. Version 59 has annotations for 1,496 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 897 disease-specific reactions organized into 447 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. 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.

New Software Released

Posted on April 12th, 2016, by robinhaw, under Reactome Announcement

analysis-interactors

The Reactome team has released new versions of the Analysis Service, Diagram Viewer, Pathway Browser analysis submission interface, and Search. These services, widgets and tools have been updated following user feedback with two main aims: to make them easier to use and to add extra features.

 The Analysis Service now has an option to perform an extended analysis that includes interaction data from IntAct, the EBI database of pairwise protein-protein interactions. Complementing this, the new version of the Diagram Viewer also features the overlay of analysis results when interactors are included.

In addition to the display of interactors from IntAct and PSICQUIC services, a new tool has been added to allow the user to upload and overlay custom interaction data onto diagrams. The tool supports different formats, explained in the in-line user guide. Uploaded data is kept across sessions in the same browser.

The main Search is aware of IntAct interactors, making them fully accessible via Reactome web interface queries. When a searched entity is not part of a Reactome pathway, it can still be found as an interactor of pathway entities based on the IntAct data. The search result will show the interactors with a list of all the curated entities that interact with them.

Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone 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 Robin Haw (Tel: 647-260-7985).

 

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. 

Updated Molecular Interaction Overlay feature now available.

Posted on February 15th, 2016, by robinhaw, under Reactome Announcement, Reactome Feature

EGFR_MIO

As part of our efforts to give our user community better experience, we have redesigned the Molecular Interaction Overlay to support quicker, easier, and more responsive access to protein-protein and protein-small molecule interaction data within the Reactome Pathway Browser.

New features and improvements include:

  • Diagram search feature includes the gene name and chemical name for interactors.
  • Interactors display name is now the gene name for proteins and the chemical name for the chemicals.
  • Tooltips are shown when hovering over the for interaction links.
  • Interactions include links to entities present in the diagram.
  • Loop-link is included when a protein/chemical interacts with itself.
  • Display option to show/hide interactors based upon a selected weighted score.
  • Crystal and chemical structures for the interactors are displayed at zoomed-in view.
  • Diagram image export for the zoomed-in view includes the protein structures in the final image.
  • Interactor file download is now available in both the Interactors toolbar and Settings panel.

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.