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). The SynGO consortium presents a framework to annotate synaptic protein locations and functions and annotations for 1,112 synaptic genes based on published experimental evidence. SynGO reports exceptional features and disease associations for synaptic genes and provides an online data analysis platform.
| Original language | English |
|---|---|
| Pages (from-to) | 217-234.e4 |
| Number of pages | 22 |
| Journal | Neuron |
| Volume | 103 |
| Issue number | 2 |
| Early online date | 3 Jun 2019 |
| DOIs | |
| Publication status | Published - 17 Jul 2019 |
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Keywords
- enrichment study
- gene annotation
- Gene Ontology
- gene set analysis
- synapse
- synaptic plasticity
- synaptic proteome network
- synaptome
- synaptopathies
Cite this
}
SynGO : An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. / Koopmans, F.; van Nierop, Pim; Andres-Alonso, M.; Byrnes, Andrea; Cijsouw, Tony; Coba, Marcelo P.; Cornelisse, L. Niels; Farrell, Ryan J.; Goldschmidt, Hana L.; Howrigan, Daniel P.; Hussain, Natasha K.; Imig, Cordelia; de Jong, Arthur P.H.; Jung, Hwajin; Kohansalnodehi, Mahdokht; Kramarz, Barbara; Lipstein, Noa; Lovering, Ruth C.; MacGillavry, Harold; Mariano, Vittoria; Mi, Huaiyu; Ninov, Momchil; Osumi-Sutherland, D.; Pielot, Rainer; Smalla, Karl Heinz; Tang, Haiming; Tashman, Katherine; Toonen, Ruud F.G.; Verpelli, Chiara; Reig-Viader, Rita; Watanabe, K.; van Weering, Jan; Achsel, Tilmann; Ashrafi, Ghazaleh; Asi, N.; Brown, Tyler C.; De Camilli, Pietro; Feuermann, Marc; Foulger, Rebecca E.; Gaudet, Pascale; Joglekar, Anoushka; Kanellopoulos, Alexandros; Malenka, Robert; Nicoll, Roger A.; Pulido, Camila; de Juan-Sanz, J.; Sheng, Morgan; Südhof, Thomas C.; Tilgner, Hagen U.; Bagni, Claudia; Bayés, Àlex; Biederer, Thomas; Brose, Nils; Chua, John Jia En; Dieterich, Daniela C.; Gundelfinger, Eckart D.; Hoogenraad, Casper; Huganir, Richard L.; Jahn, Reinhard; Kaeser, Pascal S.; Kim, Eunjoon; Kreutz, Michael R.; McPherson, Peter S.; Neale, B. M.; O'Connor, Vincent; Posthuma, Danielle; Ryan, Timothy A.; Sala, C.; Feng, Guoping; Hyman, Steven E.; Thomas, Paul D.; Smit, August B.; Verhage, Matthijs.
In: Neuron, Vol. 103, No. 2, 17.07.2019, p. 217-234.e4.Research output: Contribution to Journal › Article › Academic › peer-review
TY - JOUR
T1 - SynGO
T2 - An Evidence-Based, Expert-Curated Knowledge Base for the Synapse
AU - Koopmans, F.
AU - van Nierop, Pim
AU - Andres-Alonso, M.
AU - Byrnes, Andrea
AU - Cijsouw, Tony
AU - Coba, Marcelo P.
AU - Cornelisse, L. Niels
AU - Farrell, Ryan J.
AU - Goldschmidt, Hana L.
AU - Howrigan, Daniel P.
AU - Hussain, Natasha K.
AU - Imig, Cordelia
AU - de Jong, Arthur P.H.
AU - Jung, Hwajin
AU - Kohansalnodehi, Mahdokht
AU - Kramarz, Barbara
AU - Lipstein, Noa
AU - Lovering, Ruth C.
AU - MacGillavry, Harold
AU - Mariano, Vittoria
AU - Mi, Huaiyu
AU - Ninov, Momchil
AU - Osumi-Sutherland, D.
AU - Pielot, Rainer
AU - Smalla, Karl Heinz
AU - Tang, Haiming
AU - Tashman, Katherine
AU - Toonen, Ruud F.G.
AU - Verpelli, Chiara
AU - Reig-Viader, Rita
AU - Watanabe, K.
AU - van Weering, Jan
AU - Achsel, Tilmann
AU - Ashrafi, Ghazaleh
AU - Asi, N.
AU - Brown, Tyler C.
AU - De Camilli, Pietro
AU - Feuermann, Marc
AU - Foulger, Rebecca E.
AU - Gaudet, Pascale
AU - Joglekar, Anoushka
AU - Kanellopoulos, Alexandros
AU - Malenka, Robert
AU - Nicoll, Roger A.
AU - Pulido, Camila
AU - de Juan-Sanz, J.
AU - Sheng, Morgan
AU - Südhof, Thomas C.
AU - Tilgner, Hagen U.
AU - Bagni, Claudia
AU - Bayés, Àlex
AU - Biederer, Thomas
AU - Brose, Nils
AU - Chua, John Jia En
AU - Dieterich, Daniela C.
AU - Gundelfinger, Eckart D.
AU - Hoogenraad, Casper
AU - Huganir, Richard L.
AU - Jahn, Reinhard
AU - Kaeser, Pascal S.
AU - Kim, Eunjoon
AU - Kreutz, Michael R.
AU - McPherson, Peter S.
AU - Neale, B. M.
AU - O'Connor, Vincent
AU - Posthuma, Danielle
AU - Ryan, Timothy A.
AU - Sala, C.
AU - Feng, Guoping
AU - Hyman, Steven E.
AU - Thomas, Paul D.
AU - Smit, August B.
AU - Verhage, Matthijs
PY - 2019/7/17
Y1 - 2019/7/17
N2 - 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). The SynGO consortium presents a framework to annotate synaptic protein locations and functions and annotations for 1,112 synaptic genes based on published experimental evidence. SynGO reports exceptional features and disease associations for synaptic genes and provides an online data analysis platform.
AB - 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). The SynGO consortium presents a framework to annotate synaptic protein locations and functions and annotations for 1,112 synaptic genes based on published experimental evidence. SynGO reports exceptional features and disease associations for synaptic genes and provides an online data analysis platform.
KW - enrichment study
KW - gene annotation
KW - Gene Ontology
KW - gene set analysis
KW - synapse
KW - synaptic plasticity
KW - synaptic proteome network
KW - synaptome
KW - synaptopathies
UR - http://www.scopus.com/inward/record.url?scp=85068734308&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85068734308&partnerID=8YFLogxK
U2 - 10.1016/j.neuron.2019.05.002
DO - 10.1016/j.neuron.2019.05.002
M3 - Article
VL - 103
SP - 217-234.e4
JO - Neuron
JF - Neuron
SN - 0896-6273
IS - 2
ER -