Fireworks is new a genome-wide, hierarchical view of pathways graph supporting analysis results overlay and more. Further details on how to use the Fireworks display can be found in the Reactome User Guide.
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.
Reactome hits a major milestone: Reactome is now one of the largest freely accessible, open source pathway knowledgebases. Over the 10 years that Reactome has been curating and exporting pathway and reaction data, we’ve grown to include annotations for over 1/3 of the protein-coding genes in the current Ensembl human genome assembly. As of Version 50, Reactome comprises 7,642 human reactions involving the 7,597 protein products of 7,333 human genes, and 1,419 small molecules. These reactions are organized into 1,597 pathways, supported by 17,248 PubMed literature references. We have projected these reactions onto 99,812 orthologous proteins, creating 20,032 orthologous pathways in 19 model organisms.
New Pathways for this Release: Topics with revised content in V50 include Disease (Diseases associated with glycosaminoglycan metabolism), Gene expression (Transcriptional regulation by small RNAs and DNA methylation), Organelle biogenesis and maintenance (Mitochondrial translation), Signal Transduction (Hedgehog ‘off’ state), Transmembrane transport of small molecules (Orphan transporters), and Metabolism. We’d like to thank Renee Beekman, Caiyong Chen, Zofia M Chrzanowska-Lightowlers, Wolfgang Fischle, Long-Cheng Li, Yulu Cherry Liu, José I Martín-Subero, David S Rosenblatt, Dorothe Spillmann, Anna Stroynowska-Czerwinska who are our external reviewers.
In V49, Disease pathways have been expanded to include WNT in cancer, Uptake and function of anthrax toxins, and Processing-defective Hh variants abrogate ligand secretion. Metabolism now includes Aflatoxin activation and detoxification, and Immune system covers Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon. Development has been updated with EPH-EFN signaling. New pathways under signal transduction include Repression of Wnt target genes, VEGFA-VEGFR2 signaling, and Hedgehog ligand biogenesis. Updated signal transduction modules include TCF dependent signaling in response to WNT and Degradation of beta-catenin by the destruction complex. Mismatch Repair has beed added to DNA repair and Chromatin organization has been expanded to cover HDACs deacetylate histones, RMTs methylate histone arginines, and HDMs demethylate histones. Akira Kikuchi is our external author. Kurt Ballmer, Philipp Berger, Michael Edelbrock, Ernesto Guccione, Richard Hopkinson, Nancy Ip, Stephen Leppla, Shihui Liu, Yulu Liu, Anna Maria Masci, Mahtab Moayeri, Nishani Rajakulendran, Sima Salahshor, Christopher Schofield, Benjamin E Turk, Louise Walport, Michael Welsh, Jim Woodgett, and Xiang-Jiao Yang are our external reviewers.
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.
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:
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 biosynthesis.
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.