Reactome: A Curated Pathway Database

New Protein-protein Interaction files

Posted on June 28th, 2017, by robinhaw, under Reactome Announcement, Reactome Feature

The Reactome team has released new versions of our protein-protein interaction files derived from reactions and complexes. These files were updated following user feedback, with the goal of providing extra annotation features through support from the PSI-MITAB 2.7 data format. Interactions are computationally generated based on the data stored on complexes and reactions. The interactions provided by Reactome are not curated and are not experimental data. In addition, the complexes and reactions in species other than human are derived by orthology inference from the corresponding human complexes and reactions. Tab-delimited formatted files are also provided for human and all species.

The four new files are:

Documentation about these files is available from the Data Download page.

The former versions of the protein-protein interaction files are still available but will be removed from service as of Version 62 in September 2017. We encourage users that programmatically access these files to update the scripts.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone Medical Center, Oregon Health and Science University, 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 61 Released

Posted on June 22nd, 2017, by robinhaw, under Reactome Announcement, Reactome Release Announcement

New and Updated Pathways. 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).

Thanks to our Contributors. 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 April 20th, 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 December 21st, 2016, 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.

 

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.

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).