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.
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.
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.
The Plant Reactome group has released 21 new rice pathways, focusing on carbohydrate biosynthesis, cofactor biosnythesis, and secondary metabolite biosnythesis.
New to Reactome is Binding and Uptake of Ligands by Scavenger Receptors. Topics with new or revised events include Immune system (Fcgamma receptor (FCGR) dependent phagocytosis), Cell Cycle (Resolution of Sister Chromatid Cohesion, Regulation of PLK1 Activity at G2/M Transition, Nuclear envelope breakdown, and Initiation of Nuclear Envelope Reformation), Extracellular matrix organization (Fibronectin matrix formation and Elastic fibre formation), Metabolism (Ubiquinol biosynthesis and cytosolic-nuclear iron-sulfur cluster biogenesis), Signal Transduction (Signaling by TGF-beta Receptor Complex, Signaling by NOTCH2, and Visual phototransduction), Transmembrane transport of small molecules (Stimuli-sensing channels), and Disease (Diseases associated with visual transduction, and Signaling by NOTCH1 in cancer). New pathway illustrations for this release include Apoptosis Extrinsic pathway and Trafficking and processing of endosomal TLRs. R Lill is our external author. J Avruch, W Blaner, V Fiorito, L He, M Kawamukai, I Mattaj, S Moestrup, J Parkinson, F Rauscher, D Reinhardt, C Rosales, Y Tanno, E Tolosano, EJ Uringa, Y Watanabe, and R Weil are our external reviewers. Plant Reactome, an integrated analysis and visualization platform for plant metabolic and regulatory pathways and networks has been released. Reactome is actively soliciting feedback through a User Survey in order to assess community needs.
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.
Topics with new or revised events include Immune system (STING mediated induction of type 1 IFN and DAP12 Interactions and signaling), Disease (Mucopolysaccharidoses and Signaling by PI3K/AKT in Cancer), Cell Cycle (Golgi Cisternae Pericentriolar Stack Reorganization), Metabolism (Regulation of Cholesterol Biosynthesis by SREBP), Metabolism of proteins (Metabolism of Angiotensinogen to Angiotensins), Membrane Trafficking (GLUT4 Translocation), and Gene expression. S Alves, JL Ashworth, A Colanzi, MF Coutinho, L Jin, J Joseph, A Klip, LL Lanier, G Liang, F Rauscher, L Thorpe, Y Wang, H Yuzugullu, and J Zhao are our external reviewers. New pathway illustrations for this release include Signal Transduction, Signaling by Hippo, Signaling by SCF-KIT, and Mitochondrial Protein Import. Reactome is hosting two webinars, Using Reactome Pathway Database and Reactome Functional Interaction Network plugin in October. If you are interesting in participating, please register at Eventbrite. A new paper entitled Reactome – a curated knowledgebase of biological pathways: megakaryocytes and platelets has been published in the Journal of Thrombosis and Haemostasis.
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.
The pathway Extracellular matrix organization is new and includes Activation of Matrix Metalloproteinases. Topics with new or revised events include Immune System (Regulation of complement cascade, Trafficking and processing of endosomal TLR, Signaling by B cell receptor, and DAI mediated induction of type I IFNs), Metabolism of proteins, (Mitochondrial Protein Import), Signal transduction (Signaling by Hippo, Signaling by Notch), Circadian clock, and Gene Expression (Regulatory RNA Pathways). Sean Egan is our external author. DT Bradley , G Butler, F Delaunay, HS Earp, T Endo, L Fraczek, CA Leifer, AM Misior, ES Mocarski, CM Overall, FJ Rauscher, WA Rose, M Sudol, Y Tomari, JW Upton, and J Wienands are our external reviewers. We have created short Reactome tutorial videos that demonstrate the use of our navigation and analysis tools. New ones for this release are Pathway Browser, Pathway Analysis, and Expression Analysis. Others will be added to the Reactome YouTube Channel as they become available. Our SBML export (available here) has been enriched with a wide variety of additional annotations, including SBO terms. We have switched from using the layout extension to embedded SBGN for conveying pathway layout.
As a first step toward systematically annotating human disease processes in Reactome, a new topic, Disease, has been created. It contains the existing HIV, Influenza, Botulinum neurotoxicity, Amyloids, and Diabetes pathways with the new Signaling by EGFR in Cancer. As described in the users’ guide, pathway diagrams have been revised to show the interplay between disease and normal processes and a new color scheme has been implemented to differentiate the two. Topics with new or revised events include Immune System (ISG15 antiviral mechanism, Prolactin receptor signalling, Defensins, and Interleukin-7 signalling), Metabolism (Sulfur amino acid metabolism, Sphingolipid metabolism, O-linked glycosylation of mucins, and Serine biosynthesis), Signal transduction (Signaling by ERBB2 and Signaling by ERBB4), and Gene expression.
Annotations of chicken (Gallus gallus) DNA replication and repair, toll receptor signaling, and metabolism available at gallus.reactome.org with limited browsing and data analysis tools are now also available, with full functionality, in the Reactome pathway browser (switch species to “Gallus gallus”).
KP Ray and R Stephan are our external authors. A Ferrer, V Goffin, H Greulich, RC Harris, AM McDermott, LM Neckers, J Puck, F Rauscher, S Savas, W Xu, F Zeng, and DE Zhang are our external reviewers.