Reactome: A Curated Pathway Database

Version 57 Released

Posted on June 27th, 2016, by robinhaw, under Reactome Announcement, Reactome Release Announcement

In version V57, topics with new or revised pathways include: Developmental biology (RET signaling), Disease (Signaling by FGFR in disease and Defective CFTR causes cystic fibrosis), Gene expression (rRNA modification in the mitochondrion and Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors), Immune system (ER-Phagosome pathway, Interleukin-7 signaling, Regulation by endogenous TLR ligand, and TCR signaling), Metabolism (Lipid digestion, mobilization, and transport and Phosphate bond hydrolysis by NTPDase proteins). Metabolism of proteins (Deubiquitination), Neuronal system (Interactions of neurexins and neuroligins at synapses and SALM protein interactions at synapse). Signal transduction (EGFR downregulation, Signaling by FGFR1, and FGFRL1 modulation of FGFR1 signaling), Transmembrane transport of small molecules (ABC-family proteins mediated transport) and Vesicle-mediated transport (Clathrin-mediated endocytosis).

Our external author is Alba Sanchis. Costin AntonescuJohn Bergeron, Daniel BogenhagenNunzio BottiniGuang-Chao ChenIgor DawidRegina FluhrerNoriko GotohFrancesca GranucciRichard GrosePaul HeppenstallJing HuJan HuertasWenqin LuoMalay MandalBirgit MeldalDaniel MoralesTatsunori NishimuraRonald PetraliaGail SeaboldSunny SharmaStephanie StanfordJean SévignyPhilip WashbourneIvan Zanoni, and Valeria Zarelli are our external reviewers.

Version 56 Released

Posted on March 24th, 2016, by robinhaw, under Reactome Announcement, Reactome Release Announcement

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. 

Version 55 Released

Posted on December 15th, 2015, by robinhaw, under Reactome Announcement, Reactome Release Announcement

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 JarrousDaniel 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.

Version 54 Released

Posted on October 1st, 2015, by Matthews, under Reactome Announcement, Reactome Release Announcement

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 ChaussKatie DeCicco-SkinnerMaria 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.

Version 53 Released

Posted on July 2nd, 2015, by robinhaw, under Reactome Announcement, Reactome Release Announcement

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.

Version 52 Released

Posted on March 23rd, 2015, by robinhaw, under Reactome Announcement, Reactome Release Announcement

Melanin_Biosynthesis

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.

After 10 years Reactome hits 50!

Posted on October 8th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

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 BeekmanCaiyong ChenZofia M Chrzanowska-LightowlersWolfgang FischleLong-Cheng LiYulu Cherry Liu, José I Martín-SuberoDavid S RosenblattDorothe SpillmannAnna Stroynowska-Czerwinska who are our external reviewers.

Version 49 Released

Posted on July 15th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

In V49, Disease pathways have been expanded to include WNT in cancerUptake 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 genesVEGFA-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 histonesRMTs methylate histone arginines, and HDMs demethylate histones. Akira Kikuchi is our external author. Kurt BallmerPhilipp BergerMichael EdelbrockErnesto GuccioneRichard HopkinsonNancy IpStephen LepplaShihui LiuYulu LiuAnna Maria MasciMahtab MoayeriNishani RajakulendranSima SalahshorChristopher SchofieldBenjamin E TurkLouise WalportMichael WelshJim Woodgett, and Xiang-Jiao Yang are our external reviewers.

Version 48 Released

Posted on March 27th, 2014, by robinhaw, under Reactome Announcement, Reactome Release Announcement

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.