Reactome is hosting a new series of webinars that will introduce the website and our suite of pathway and network visualization and analysis tools. Two sessions have been scheduled for December.
The first webinar on Monday 2nd December will describe Using Reactome Pathway Database. On Thursday 5th December, the second session will introduce the Reactome Functional Interaction Network Cytoscape plugin. If you are interesting in participating, please register at Eventbrite.
Feel free to pass this invitation along to colleagues who may benefit from learning about Reactome.
Registrants will receive detailed instructions about accessing the webinar via e-mail the Friday prior to the event. (Anyone registering between Friday and the close of registration will receive the message shortly after the registration is received, within normal business hours.)
A new version of Pathway Commons, which is a collection of publically available human pathways and interaction databases has been released.
A paper describing the new Reactome web interface, pathway browser, and analysis tools has been published online in the Database Issue of Nucleic Acids Research.
David Croft and Robin Haw from Reactome, Abigail Cabunoc from WormBase, and Ameila Ireland from GMOD are at the Google Summer of Code Mentor’s Summit, this weekend, at Googleplex Mountain View, CA.
Reactome is one of nine project partners who will be participating in the ORCID Adoption and Integration (A&I) Program, which is funded by the Alfred P. Sloan Foundation. ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. Reactome depends on collaborations with outside experts to assemble and peer-review its pathway modules. The integration of ORCID within Reactome enables us to meet a key challenge with authoring and curating biological information by incentivizing and crediting the external experts that contribute their expertise and time to the Reactome curation process.
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.
Topics with new or revised events include Disease (Defects in biotin metabolism, Defects in cobalamin (B12) metabolism and TGF-beta receptor complex signaling in cancer), Signal transduction (Signaling by Leptin), Extracellular matrix organization (Degradation of the extracellular matrix, Laminin interactions, and Integrin cell surface interactions), Transmembrane transport of small molecules (TRP channels), Cell cycle (Regulation of PLK1 activity at G2/M transition), and Cellular response to stress (Cellular senescence). Rosemary J Akhurst, Wytse Bruinsma, Lei He, Dominique Meyer, Steven W Polyak, Sylvie Ricard-Blum, Shamith Samarajiwa, Thomas Scherer, and David Watkins are our external reviewers. Plant Reactome has released a new batch of rice pathways associated with cofactor biosynthesis, hormone biosnythesis, and fatty acids & lipids biosynthesis. Examples include: pyridoxamine anabolism, ABA biosynthesis and mediated signaling and glycolipid desaturation. The Reactome FI plugin, which was designed to find network patterns related to cancer and other types of diseases within a gene list, has been upgraded to support Cytoscape v3, and is now available at the Cytoscape app store.
ISMB2013 is in Berlin this year and Reactome will be there. Robin Haw will be talking at the Network Biology SIG Meeting on Friday, July 19th and presenting a poster at the main ISMB conference (A078).
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.
New topics are Reproduction (Fertilization) and SUMOylation (Processing and activation of SUMO). Topics with new or revised events include Apoptosis (Extrinsic Pathway for Apoptosis), Binding and Uptake of Ligands by Scavenger Receptors, Cell Cycle (Nuclear Pore Complex (NPC) Disassembly), Disease (Assembly Of The HIV Virion and Budding and maturation of HIV virion), Extracellular matrix organization (Non-integrin membrane-ECM interactions and ECM proteoglycans, Immune System (Complement cascade, Cytosolic sensors of pathogen-associated DNA, and Fc epsilon receptor (FCERI) signaling), Metabolism (Metabolism of vitamins and cofactors), Signal transduction (The phototransduction cascade, Signaling by NOTCH2, Signaling by GPCR, and Signaling by Wnt).
R Belew and A Niarakis are our external authors. W Antonin, M Boutros, S Boyle, DT Bradley, M Dubé, EJ Fuentes, AK Garg, MX Ilagan, L Jin, P Lishko, CL Makino, N Venkatesan, C Neyen, C Pop, S Ricard-Blum, R Roncagalli, GS Salvesen, and J Wu are our external reviewers.