As part of our continuous effort to give our user community better experience, we have updated the Reactome Pathway Browser to support a faster, smoother, and more responsive Gene Expression Atlas (GXA) feature.
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 Belaya, Gregg Duester, Joao Goncalves, Shihui Liu, Yulu Cherry Liu, Esben Lorentzen, Andrew Mumford, Toshio Nakaki, Joseph Napoli, Kuniaki Saito, Shashi 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.
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 Beekman, Caiyong Chen, Zofia M Chrzanowska-Lightowlers, Wolfgang Fischle, Long-Cheng Li, Yulu Cherry Liu, José I Martín-Subero, David S Rosenblatt, Dorothe Spillmann, Anna Stroynowska-Czerwinska who are our external reviewers.
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.
In V49, Disease pathways have been expanded to include WNT in cancer, Uptake 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 genes, VEGFA-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 histones, RMTs methylate histone arginines, and HDMs demethylate histones. Akira Kikuchi is our external author. Kurt Ballmer, Philipp Berger, Michael Edelbrock, Ernesto Guccione, Richard Hopkinson, Nancy Ip, Stephen Leppla, Shihui Liu, Yulu Liu, Anna Maria Masci, Mahtab Moayeri, Nishani Rajakulendran, Sima Salahshor, Christopher Schofield, Benjamin E Turk, Louise Walport, Michael Welsh, Jim Woodgett, and Xiang-Jiao Yang are our external reviewers.
The Molecules tab in the Pathway Browser now has improved interactivity and usability, allowing users to easily list or download all molecule information from the currently displayed Pathway Diagram.
Two new Reactome papers entitled “A controlled vocabulary for pathway entities and events” and “ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis” have been published in DATABASE and F1000Research, respectively. More publications from the Reactome Team can be found here.
Pathway databases, like Reactome, are uniquely suited for interpreting the results of high-throughput functional genomics data sets such as microarray-based expression profiles, protein interaction sets, and chromatin IP. In response to user feedback and new feature requests, we have released a new Reactome Pathway Browser with an integrated suite of tools for pathway analysis. Using these improved features, you can map protein lists to Reactome pathways, perform pathway overrepresentation analysis for a set of genes, colourize pathway diagrams with gene expression data, and compare model organism and human pathways. To support third-party tool integration, the Reactome Pathway Analysis Portal is also available via RESTful web services. Further details about the new pathway analysis tool can be found in our User Guide.
New in V48 is Organelle biogenesis (Mitochondrial biogenesis). Topics with new or updated pathways include Cell cycle (Depolymerisation of the nuclear lamina), Cellular responses to stress (Cellular responses to heat stress, Development (Transcriptional regulation of pluripotent stem cells, Disease (Glycogen storage diseases (Myoclonic epilepsy of Lafora) and Neurotoxicity of clostridium toxins), Gene expression (Epigenetic regulation of gene expression), Metabolism of proteins (O-glycosylation of TSR domain-containing proteins and Sialic acid metabolism), and Signal transduction (TCF-dependent signaling in response to WNT. The Gallus gallus pathway Innate immune system has been updated to include Complement cascade. Luciano Di Croce, Matyas Gorjanacz, Ingrid Grummt, Angela M Lezza, Juan F Medrano, Mridul Mukherji, Bibhusita Pani, Bartholomew Pederson, Gerd Pfeifer, Nishani Rajakulendran, Yih-Horng Shiao, Renee van Amerongen, Renate Voit, Jianlong Wang, and Saumya Wickramasinghe are our external reviewers.
New in V47 is Chromatin organization (Chromatin modifying enzymes). Topics with new or revised events include Cellular response to stress (Cellular senescence and Detoxification of reactive oxygen species, Cell cycle (Condensation of prophase chromosomes), Immune system (Cell surface interaction at the vascular wall), Metabolism of proteins (Synthesis of dolichyl-phosphate), and Signal transduction (Beta-catenin independent WNT signaling). Brenda Gallie, is our external author. Tom Karagiannis, Mahendra Kavdia, Akira Kikuchi, Michelle Longworth, Shamith Samarajiwa, and Jaap Jan Zwaginga are our external reviewers.