Dataset Information

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

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).

SUBMITTER: Koopmans F

PROVIDER: S-EPMC6764089 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

Koopmans Frank F van Nierop Pim P Andres-Alonso Maria M Byrnes Andrea A Cijsouw Tony T Coba Marcelo P MP Cornelisse L Niels LN Farrell Ryan J RJ Goldschmidt Hana L HL Howrigan Daniel P DP Hussain Natasha K NK Imig Cordelia C de Jong Arthur P H APH Jung Hwajin H Kohansalnodehi Mahdokht M Kramarz Barbara B Lipstein Noa N Lovering Ruth C RC MacGillavry Harold H Mariano Vittoria V Mi Huaiyu H Ninov Momchil M Osumi-Sutherland David D Pielot Rainer R Smalla Karl-Heinz KH Tang Haiming H Tashman Katherine K Toonen Ruud F G RFG Verpelli Chiara C Reig-Viader Rita R Watanabe Kyoko K van Weering Jan J Achsel Tilmann T Ashrafi Ghazaleh G Asi Nimra N Brown Tyler C TC De Camilli Pietro P Feuermann Marc M Foulger Rebecca E RE Gaudet Pascale P Joglekar Anoushka A Kanellopoulos Alexandros A Malenka Robert R Nicoll Roger A RA Pulido Camila C de Juan-Sanz Jaime J Sheng Morgan M Südhof Thomas C TC Tilgner Hagen U HU Bagni Claudia C Bayés Àlex À Biederer Thomas T Brose Nils N Chua John Jia En JJE Dieterich Daniela C DC Gundelfinger Eckart D ED Hoogenraad Casper C Huganir Richard L RL Jahn Reinhard R Kaeser Pascal S PS Kim Eunjoon E Kreutz Michael R MR McPherson Peter S PS Neale Ben M BM O'Connor Vincent V Posthuma Danielle D Ryan Timothy A TA Sala Carlo C Feng Guoping G Hyman Steven E SE Thomas Paul D PD Smit August B AB Verhage Matthijs M

Neuron 20190603 2

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 ...[more]

PMID: 31171447

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Project description:BackgroundMicrobes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds.ResultsIn this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that "fatty acids", "terpenoids", and "shikimates and phenylpropanoids" accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities.ConclusionsMCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com . This database may serve as a useful resource for synthetic biologists.

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Dataset Information

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

Publications

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

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