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Koopmans F, van Nierop P, Andres-Alonso M, Byrnes A, Cijsouw T, Coba MP, Cornelisse LN, Farrell RJ, Goldschmidt HL, Howrigan DP, Hussain NK, Imig C, de Jong APH, Jung H, Kohansalnodehi M, Kramarz B, Lipstein N, Lovering RC, MacGillavry H, Mariano V, Mi H, Ninov M, Osumi-Sutherland D, Pielot R, Smalla KH, Tang H, Tashman K, Toonen RFG, Verpelli C, Reig-Viader R, Watanabe K, van Weering J, Achsel T, Ashrafi G, Asi N, Brown TC, De Camilli P, Feuermann M, Foulger RE, Gaudet P, Joglekar A, Kanellopoulos A, Malenka R, Nicoll RA, Pulido C, de Juan-Sanz J, Sheng M, Südhof TC, Tilgner HU, Bagni C, Bayés À, Biederer T, Brose N, Chua JJE, Dieterich DC, Gundelfinger ED, Hoogenraad C, Huganir RL, Jahn R, Kaeser PS, Kim E, Kreutz MR, McPherson PS, Neale BM, O'Connor V, Posthuma D, Ryan TA, Sala C, Feng G, Hyman SE, Thomas PD, Smit AB, Verhage M. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron 2019; 103:217-234.e4. [PMID: 31171447 DOI: 10.1016/j.neuron.2019.05.002] [Citation(s) in RCA: 360] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/02/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022]
Abstract
Synapses are fundamental information-processing units of the brain, and synaptic dysregulation is central to many brain disorders ("synaptopathies"). However, systematic annotation of synaptic genes and ontology of synaptic processes are currently lacking. We established SynGO, an interactive knowledge base that accumulates available research about synapse biology using Gene Ontology (GO) annotations to novel ontology terms: 87 synaptic locations and 179 synaptic processes. SynGO annotations are exclusively based on published, expert-curated evidence. Using 2,922 annotations for 1,112 genes, we show that synaptic genes are exceptionally well conserved and less tolerant to mutations than other genes. Many SynGO terms are significantly overrepresented among gene variations associated with intelligence, educational attainment, ADHD, autism, and bipolar disorder and among de novo variants associated with neurodevelopmental disorders, including schizophrenia. SynGO is a public, universal reference for synapse research and an online analysis platform for interpretation of large-scale -omics data (https://syngoportal.org and http://geneontology.org).
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Affiliation(s)
- Frank Koopmans
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands; Department of Molecular and Cellular Neurobiology, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Pim van Nierop
- Department of Molecular and Cellular Neurobiology, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Maria Andres-Alonso
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group "Dendritic Organelles and Synaptic Function," ZMNH, University MC, Hamburg, 20251, Germany
| | - Andrea Byrnes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tony Cijsouw
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Marcelo P Coba
- Zilkha Neurogenetic Institute and Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90333, USA
| | - L Niels Cornelisse
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Ryan J Farrell
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hana L Goldschmidt
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel P Howrigan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Natasha K Hussain
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Cordelia Imig
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Arthur P H de Jong
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hwajin Jung
- Center for Synaptic Brain Dysfunctions, IBS, and Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Mahdokht Kohansalnodehi
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Barbara Kramarz
- Functional Gene Annotation, Institute of Cardiovascular Science, UCL, London WC1E 6JF, UK
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Ruth C Lovering
- Functional Gene Annotation, Institute of Cardiovascular Science, UCL, London WC1E 6JF, UK
| | - Harold MacGillavry
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Huaiyu Mi
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Momchil Ninov
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Rainer Pielot
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Karl-Heinz Smalla
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Haiming Tang
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Katherine Tashman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruud F G Toonen
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Chiara Verpelli
- CNR Neuroscience Institute Milan and Department of Biotechnology and Translational Medicine, University of Milan, 20129 Milan, Italy
| | - Rita Reig-Viader
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, 08025 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain
| | - Kyoko Watanabe
- Department Complex Trait Genetics, CNCR, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands; Department of Clinical Genetics, UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Jan van Weering
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Ghazaleh Ashrafi
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nimra Asi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tyler C Brown
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pietro De Camilli
- Departments of Neuroscience and Cell Biology, HHMI, Kavli Institute for Neuroscience, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Marc Feuermann
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Rebecca E Foulger
- Functional Gene Annotation, Institute of Cardiovascular Science, UCL, London WC1E 6JF, UK
| | - Pascale Gaudet
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Anoushka Joglekar
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Alexandros Kanellopoulos
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Robert Malenka
- Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Roger A Nicoll
- Departments of Cellular and Molecular Pharmacology and Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Camila Pulido
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jaime de Juan-Sanz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Morgan Sheng
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hagen U Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, 08025 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - John Jia En Chua
- Department of Physiology, Yong Loo Lin School of Medicine and Neurobiology/Ageing Program, Life Sciences Institute, National University of Singapore and Institute of Molecular and Cell Biology, A(∗)STAR, Singapore, Singapore
| | - Daniela C Dieterich
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Eckart D Gundelfinger
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Casper Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Richard L Huganir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Pascal S Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, IBS, and Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group "Dendritic Organelles and Synaptic Function," ZMNH, University MC, Hamburg, 20251, Germany
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Ben M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vincent O'Connor
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Danielle Posthuma
- Department Complex Trait Genetics, CNCR, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands; Department of Clinical Genetics, UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Timothy A Ryan
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carlo Sala
- CNR Neuroscience Institute Milan and Department of Biotechnology and Translational Medicine, University of Milan, 20129 Milan, Italy
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven E Hyman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - Matthijs Verhage
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands.
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