The Reactome team has released new versions of the Analysis Service, Diagram Viewer, Pathway Browser analysis submission interface, and Search. These services, widgets and tools have been updated following user feedback with two main aims: to make them easier to use and to add extra features.
The Analysis Service now has an option to perform an extended analysis that includes interaction data from IntAct, the EBI database of pairwise protein-protein interactions. Complementing this, the new version of the Diagram Viewer also features the overlay of analysis results when interactors are included.
In addition to the display of interactors from IntAct and PSICQUIC services, a new tool has been added to allow the user to upload and overlay custom interaction data onto diagrams. The tool supports different formats, explained in the in-line user guide. Uploaded data is kept across sessions in the same browser.
The main Search is aware of IntAct interactors, making them fully accessible via Reactome web interface queries. When a searched entity is not part of a Reactome pathway, it can still be found as an interactor of pathway entities based on the IntAct data. The search result will show the interactors with a list of all the curated entities that interact with them.
Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.
Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!
For more information please contact Robin Haw (Tel: 647-260-7985).
Topics with new or revised content in V56 include Cell cycle (AURKA activation by TPX2, Interaction between PHLDA1 and AURKA, and The role of GTSE1 in G2/M progression after G2 checkpoint) , Disease (Diseases associated with O-glycosylation of proteins), Gene expression (ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression, Major pathway of rRNA processing in the nucleus, RNA polymerase II transcribes snRNA genes, rRNA modification in the nucleus, and Transcriptional Regulation by TP53), Immune system (Signaling by Interleukins and related cytokines), Metabolism, Metabolism of proteins (Cooperation of PDCL and TRiC/CCT in G-protein beta folding), Neuronal system (SALM protein interactions at synapse), and signal transduction (Amine ligand-binding receptors, Chemokine receptors bind chemokines, ERBB2 regulates cell motility, FGFR2 alternative splicing, G alpha (s) signaling events, PI5P, PP2A and IER3 regulate AKT signaling, and Signaling by PTK6).
Ali Badache, Alexander Bird, Helen Chen, Richard P Grose, Hiren J Joshi, Lars Hansen, Nouria Hernandez, Sebastian Iben, Alberto Inga, Eunjoon Kim, Erin J Adams, Adrienne Luoma, Christopher A Maxwell, Birgit Meldal, Isabel Pires, Francoise Porteu, Robin Reed, Ana Rondon, Kavita Shah, Sunny Sharma, Nicholas G Vincent, Karen Vousden, Barry M Willardson, Stuart A Wilson, Sara Zaccara, and Dirk Zajonc are our external reviewers.
As part of our efforts to give our user community better experience, we have redesigned the Molecular Interaction Overlay to support quicker, easier, and more responsive access to protein-protein and protein-small molecule interaction data within the Reactome Pathway Browser.
New features and improvements include:
- Diagram search feature includes the gene name and chemical name for interactors.
- Interactors display name is now the gene name for proteins and the chemical name for the chemicals.
- Tooltips are shown when hovering over the for interaction links.
- Interactions include links to entities present in the diagram.
- Loop-link is included when a protein/chemical interacts with itself.
- Display option to show/hide interactors based upon a selected weighted score.
- Crystal and chemical structures for the interactors are displayed at zoomed-in view.
- Diagram image export for the zoomed-in view includes the protein structures in the final image.
- Interactor file download is now available in both the Interactors toolbar and Settings panel.
In version V55, topics with new or revised pathways include: Developmental biology (Activation of anterior HOX genes in hindbrain development during early embryogenesis), Disease (ABC transporter diseases), Gene expression (B-WICH complex positively regulates rRNA expression and tRNA processing), Hemostasis (updated Cell surface interaction at the vascular wall and GPVI-mediated activation cascade), Immune system (IL-6 family signaling and Regulation of BCR signaling by CD22), Metabolism (Response to metal ions, Selenoamino acid synthesis and metabolism as well as updates to Complex I biogenesis and Metabolism of fat-soluble vitamins). Metabolism of proteins has been updated to include Protein repair as well as revisions to Amyloid fiber formation and SUMOylation. Cellular responses to stress includes an update to Macroautophagy, Muscle contraction has been expanded to include Cardiac conduction. Signal transduction includes updates to the RHO GTPases Activate NADPH Oxidases pathway, and Vesicle-mediated transport now covers COPI-mediated anterograde traffic.
Our external author is René Rezsohazy. Jan-Willem Akkerman, Sílvia Atrian, Angela Bachi, Francesco Blasi, Gianni Colotti, Giuseppe Filosa, David Fisher, Yaron Galanty, Nayef Jarrous, Daniel Klionsky,Taco Kuijpers, Rakesh Kumar, Birgit Meldal, Masashi Narazaki , James Paulson, Piergiorgio Percipalle, George Perry, Chris Powell, Mark Rush, Suneet Shukla, Guntram Suske, Tsutomu Suzuki, Toshio Tanaka, and Xiang-Dong Zhang are our external reviewers.
In version V54, the topic Mitophagy has been added. New disease pathways include SLC transporter disorders, Essential pentosuria, Diseases associated with surfactant metabolism, Pentose phosphate pathway disease, and Glycogen storage diseases. Updated DNA repair pathways include Double-strand break repair, Nucleotide excision repair, and the Fanconi anemia pathway. Gene expression now covers tRNA processing and immune system annotations have been expanded to include MAP3K8 (TPL2)-dependent MAPK1/3 activation as well as updates to the Immunoregulatory interactions between a lymphoid and a non-lymphoid cell pathway. Under Metabolism, Surfactant metabolism and Catabolism of glucuronate to xylulose-5-phosphate have been added and Fructose metabolism has been revised. Metabolism of proteins includes additions to the Amyloid formation pathway. Signal transduction includes updates to the TNF signaling pathway and Vesicle-mediated transport now covers Cargo concentration in the ER as well as additions to COPII (Coat protein 2) mediated vesicle transport.
New pathway Illustrations are available for Asparagine N-linked glycosylation and DNA repair.
Alexander Barrow, James Borowiec, Stefan Bröer, Daniel Chauss, Katie DeCicco-Skinner, Maria Fousteri, Kasper Fugger, Marc Kantorow, Louis Levinger, Yuri Motorin, and Harald Wajant are our external reviewers. João Ribeiro and José Carlos Cameselle have revised pathways for Reactome.
Gramene is pleased to announce the release of the new Plant Reactome pathway database website at http://gramene.org/release-notes-47. This milestone is the highlight of Gramene release #47. New Plant Reactome features include pathway analysis tools for researchers and an intuitive, menu-driven front page with quick links to the pathway browser, search features, and tutorials. The analysis tools allow researchers to upload gene lists, Uniprot IDs, compound identifiers, and/or -omics expression studies to see their data displayed on the Plant Reactome pathway model along with a pathway enrichment analysis. Inter-species pathway comparisons and advanced search features are also available. The Plant Reactome is a database of plant metabolic and regulatory pathways, and currently provides over 200 manually curated Oryza sativa pathways, plus projections to 33 other plant species with
sequenced genomes and transcriptomes.
A complete description of the contents of this new release is available in our release notes (http://gramene.org/release-notes-47).
Please let us know (http://tools.gramene.org/feedback) if you have questions or suggestions.
The Gramene Team
In version V53, signal transduction pathways have been updated to include mTOR signaling, MAPK6/MAPK4 signaling, the RAF/MAPK pathway and Deactivation of the beta-catenin transactivating complex.
New immune system pathway include the TNFRSF mediated non-canonical NF-kB pathway and Immunoregulatory interactions between Lymphoid and a non-Lymphoid cells.
New disease pathways are Diseases associated with glycosylation precursor biosynthesis and ABC transporter diseases.
Other revised topics include Cellular responses to stress (Macroautophagy), Chromatin organization (HDMs demethylate histones) and developmental biology (LGI-ADAM interactions).
New pathway Illustrations are available for Cellular Senescence, Oncogene Induced Senescence, Oxidative Stress Induced Senescence, DNA Damage/Telomere Stress Induced Senescence, Senescence-Associated Secretory Phenotype (SASP).
Alexander Barrow, Sharon A Tooze, Vincent Harley, Richard Hopkinson, Simon Mathien, Dies Meijer, Sylvain Meloche, Ugo Moens, Karobi Moitra, Akhil Rajput, Robert Roskoski, Christopher Schofield, Ole-Morten Seternes, Mathilde Soulez, Dorothe Spillmann, David J Timson, Richard Virgen-Slane, Louise Walport, Carl F Ware, and Fried Zwartkruis are our external reviewers.
In version V52, Reactome has broadened its coverage of Disease to include Hereditary fructose intolerance, Essential fructosuria, Intestinal disaccharidase deficiencies, and Diseases associated with TLR signaling cascade.
New Metabolic pathways include Fructose biosynthesis, Lactose synthesis, and Melanin biosynthesis and Post-translational protein modification has been expanded to cover SUMOylation of DNA damage response and repair proteins.
The DNA repair pathways Base excision repair, DNA damage bypass, and DNA damage reversal have been revised and within Signal transduction, RHO GTPase Effectors is new and Deactivation of the beta-catenin transactivating complex has been updated.
New pathways have also been added to the topics of Gene Expression (TP53 regulates metabolic genes), Immune system (C-type lectin receptors (CLRs), Chromatin organization (PKMTs methylate histone lysines), and Programmed cell death (Regulated necrosis).
New pathway Illustrations are available for Circadian clock, DNA replication, DNA strand elongation, Immune system, Innate immune system, Membrane trafficking, Muscle contraction, and Visual phototransduction.
Francisco Rivero is our external author.
Mahdi Amiri, James Borowiec, Francis Ka-Ming Chan, Marco d’Ischia, Stefano Ferrari, Teunis Geijtenbeek, Paul Hwang, Shosuke Ito, Ju-Gyeong Kang, Douglas McDonald, Mo Motamedi, Hassan Naim, David Timson, Dean Tolan, Ping-Yuan Wang, and Aaron Zorn are our external reviewers.
Reactome comprises 8,169 human reactions involving the 8,183 protein products of 7,954 human genes, and 1,449 small molecules. These reactions are organized into 1,762 pathways, supported by 18,900 PubMed literature references. We have projected these reactions onto 98,602 orthologous proteins, creating 19,039 orthologous pathways in 18 model organisms.