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.
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!
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.
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.
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.