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.
Reactome has released a new web interface for its open-source curated database of pathways and reactions. The redesigned web site is a faster, more flexible tool to query, analyze and visualize pathway and network data. New features include:
- Access to visualization and data analysis tools via a simpler home page.
- New data model and visualization strategies to annotate and display disease counterparts of normal human processes, supporting descriptions of diseases due to infection and mutation at the molecular level.
- Revised event hierarchy panel to provide interactivity and access to the entire listing of all the Reactome pathways.
- Improved flexibility and performance of our pathway browser with a new pathway diagram visualization tool using HTML5 Canvas.
- Extended data overlaying technologies to support molecular interaction data from the PSIQUIC registry, including BindingDB, DrugBank, and GeneMANIA.
- New pathway diagram tools to search within the displayed pathway, overlay the pathway with functional interactors, and download the diagram as a snapshot or PNG file.
- Enhanced “Details” panel providing alternative displays of graphical and textual information, such as 3D structural data and citations for proteins from PDB, for small molecules from ChEBI, for the stoichiometry of metabolic reactions from Rhea, and for expression data from Gene Expression Atlas.
- Merged pathway identifier mapping, over-representation, and expression analysis tools into a tabbed data analysis portal with integrated visualization for improved pathway diagram colorization with user-supplied experimental data.
- Updated Reactome Functional Interaction plugin supports Cytoscape v3.x., providing useful tools for the discovery of network patterns related to cancer and other types of disease.
Reactome is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center, and The European Bioinformatics Institute. Freely available to all users worldwide, the Reactome database offers human pathway data that span and integrate metabolism, signaling cascades, and cellular processes like apoptosis, extracted from the published literature in collaboration with experts from the scientific community and cross-referenced to a wide range of biological databases. Reactome data and software are distributed under the terms of the Creative Commons Attribution 3.0 Unported License.
Reactome often needs to represent a protein in several different forms, perhaps the initial translated form, then as fragments of this following processing, or following many different kinds of post-translational modification. In response to this, we have developed a systematic nomenclature for the names of peptides.
As part of the systematic renaming of Reactome pathway components, we have used HGNC gene symbols as the label for gene products. These are identified from UniProt via the Reactome reference molecule.
Reactome often represents several peptides that are derived from the same translated protein, all sharing a common UniProt external reference. To generate unique names for these, we have added the start and end coordinates of the peptide as a suffix to the gene symbol. The coordinates of the Reactome peptide are compared with UniProt’s ‘Chain’ feature; in UniProt this feature is part of an annotation group called Molecular Features. This feature is used because it represents the ‘default’ peptide; this usage is consistent with our use of Uniprot IDs as our primary external peptide reference. If the start and end coordinates of the Reactome peptide agree with the Uniprot Chain feature, the coordinates are not added to the gene symbol. If either coordinate is not the same as the Chain feature, both Reactome coordinates are added as a gene symbol suffix. When the true peptide start or end coordinates are unknown, the ‘?’ symbol is used. This combination of gene symbol plus coordinates is usually sufficient to generate a unique name.
Post-translational modifications (PTMs) are shown as a prefix to the gene symbol. Some Reactome peptides are exempt from systematic renaming and are named in a style that is similar to the systematic style, so far as possible.
A full explanation of the renaming process is available on the Reactome Wiki.
Topics with new or revised events include Immune system (TLR4 cascade, MyD88:Mal cascade on plasma membrane, and MyD88-independent cascade), Cell Cycle (Condensation of prometaphase chromosomes, Mitotic prophase: MASTL facilitates mitotic progression, and Resolution of sister chromatid cohesion), Extracellular matrix organization (Collagen degradation, Elastic fibre formation, and Assembly of collagen fibrils and other multimeric structures), Metabolism (Inositol Phosphate Metabolism, Arachidonic acid metabolism, Mitochondrial Iron-Sulfur Cluster Biogenesis, and Phosphate bond hydrolysis by NUDT proteins), Signal Transduction (Signaling by Activin and Signaling by IGF1R), and Gene expression. New pathway illustrations for this release include Cell Cycle and Apoptosis. R Lill is our external author. A Burgess, YG Chen, KA Fitzgerald, F Granucci, M Holzenberger, R Ito, S Kalamajski, V Malhotra, V Mochida, L Muiznieks, J Napetschnig, S Raleigh, F Rauscher, S Ricard-Blum, TA Rouault, M Rush, T Sorsa, WH Tong, T Wundenberg, I Zanoni, and N Zhang are our external reviewers. Reactome’s SBML export (available here) has been upgraded to Level2 Version4. Our SOAP and RESTful web services, have been moved to a new server. A new series of webinars, which will introduce the Reactome website and our suite of pathway and network visualization and analysis tools, will restart in January 2013. Registration details can be found on EventBrite. A new paper, describing the extension of the Reactome data model and enhancing the web tools to permit the annotation and visualization of protein variants, anti-cancer therapeutics, and other disease processes using Reactome, was published in Cancers.
New in Version 41 is the topic Cellular responses to stress, including Regulation of Hypoxia-inducible Factor by oxygen. Topics with new or revised events include Immune System (MHC Class II mediated antigen processing & presentation), Metabolism (Abacavir transport and metabolism, Glycerophospholipid biosynthesis, Glycosaminoglycan metabolism, Linoleic acid and alpha-linolenic acid metabolism, O2/CO2 exchange in erythrocytes, PI Metabolism, Reversible hydration of carbon dioxide, and Activation of arylsufatases), Signal transduction (Signaling by TGF-beta Receptor Complex and Gastrin-CREB signalling pathway via PKC and MAPK), Extracellular matrix organization (Collagen biosynthesis and modifying enzymes) and Gene expression. New Disease pathways include Abnormal metabolism in phenylketonuria, Latent infection of H. sapiens with Mycobacterium tuberculosis, and Signaling by FGFR in disease. R Stephan and S Tripathi are our external authors. EG Canty-Laird, S Ezzat, T Huang, J Neefjes, K Rantanen, F Rauscher, M Wakelam are our external reviewers. Based upon feedback from our users, Reactome has started to provide Pathway Illustrations. New ones for this release are: Signaling by EGFR, Hemostasis, Respiratory Electron Transport System, RAF/MAP kinase cascade, Signaling by NGF, PIP3 activates AKT signaling, Signaling by FGFR, Signaling by Insulin receptor, Signaling by BMP, Signaling by TGF beta, Signaling by Notch, Pre-NOTCH Expression and Processing, Signaling by NOTCH1, NOTCH2, NOTCH3, and NOTCH4, Signaling by PDGF, Integrin cell surface interactions, Signaling by ERBB2 and ERBB4. For the systems biology community, we now offer SBGN export for all pathways. Our SBGN is generated using libSBGN Milestone 2. Protein pages in Reactome now include link outs to GeneCards annotations. An updated Reactome tutorial has been published in Current Protocols in Bioinformatics.
Reactome has a new RESTful interface, which has the ability to expose pathway data in Reactome as XML and JSON.
If you would prefer to use our old website, the classic Reactome home page, displaying the reactionmap (or “starry sky”) is still available. The old website is still functional but will no longer being maintained, and will become progressively more out of date. We recommend that you use the new Reactome homepage.
Recently, Reactome released a new website and an updated suite of data analysis tools. Many users of our pathway analysis tools have asked if we will continue to support the skypainter analysis tool. The skypainter tool is available at http://www.reactome.org/cgi-bin/skypainter2. We are also working on resurrecting the classic Reactome website.
The reactionmap (or “starry sky”) and the skypainter tool are still functional but are no longer being actively maintained, and will become progressively more out of date. Please use either the “Pathway Analysis” or the “Expression Analysis” buttons provided on new Reactome homepage.
Reactome provides orthology-based pathway projections from human to other species. We are currently reviewing the list of target species. Please let us know if you would like to include a species that’s not in the planned target species list.
Reactome is committed to providing access to high-quality pathway information and useful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools. You can access the survey at: http://tinyurl.com/l48zzq. Thanks for taking part.