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.
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.
We have released a new version of the Reactome FI Cytoscape plugin: 4.0.0 beta. This version provides a suite of features to help users to explore Reactome pathways directly in Cytoscape. Using these features, you can load pathways in the Reactome database into Cytoscape, visualize Reactome pathways in either the native pathway diagram view or the FI network view, do pathway enrichment analysis for a set of genes, and check genes from your list in identified pathways.
Read more about the Reactome FI Cytoscape Plugin here.
The Gramene/Plant Reactome team will be presenting a workshop at the Plant and Animal Genomes (PAG 2014) Conference! Learn the latest updates to Gramene’s comparative genomics and pathways visualization/mining tools to aid your research of plant models and crops.
Workshops will give a broad overview of Gramene’s database resources and demonstrate many specific topics like how to:
- Explore plant reference genomes with value-added functional annotation, population data, and phylogenomic comparisons
- Navigate metabolic and regulatory pathways with the new Plant Reactome
- Analysis of gene expression datasets on Plant Reactome
- Visualize your data on Gramene’s genome and pathway browsers
- Mine mutant genes from our extensive germplasm genotype database
- Download images, sequences, orthologs, gene-trees, and many other data in a variety of conventional formats
- Give feedback and get help!
Meet with Gramene staff and developers to explore what Gramene can do for you.
Also please VISIT OUR BOOTH for one-on-one assistance or just to say Hi!