The University of Southampton
University of Southampton Institutional Repository
Warning ePrints Soton is experiencing an issue with some file downloads not being available. We are working hard to fix this. Please bear with us.

SynGO: an evidence-based, expert-curated knowledge base for the synapse

SynGO: an evidence-based, expert-curated knowledge base for the synapse
SynGO: an evidence-based, expert-curated knowledge base for the synapse

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.

enrichment study, gene annotation, Gene Ontology, gene set analysis, synapse, synaptic plasticity, synaptic proteome network, synaptome, synaptopathies
0896-6273
217-234.e4
Koopmans, Frank
ad55cb7b-0d2a-4fb2-9979-39fef93cfbab
van Nierop, Pim
39ec73cc-0f66-4408-a3a3-ea5adc40d258
Andres-Alonso, Maria
f39dfd55-bb9d-4f9e-9290-161dbbc2c3a2
Byrnes, Andrea
63034b4f-cd0c-4cc4-9103-0177ed3f5a75
Cijsouw, Tony
d53f782a-5249-4d9d-acf4-b91acf9418ed
Coba, Marcelo P.
b2c97251-abe6-46f0-98d4-86d8b2dae2b4
Cornelisse, L. Niels
75489a0b-1a34-4efa-9321-8ea4bb631679
Farrell, Ryan J.
2d6aabca-4aa2-48d1-bfb7-66accb790157
Goldschmidt, Hana L.
1101d02f-86e3-4d05-8d4e-0d5391ab946f
Howrigan, Daniel P.
cb4cafba-d5be-4d48-9f6b-d2a0a795418d
Hussain, Natasha K.
06f25c3c-6481-48de-bc4e-6c677198c20e
Imig, Cordelia
7029499e-53a2-482c-964c-40b17ec920bb
de Jong, Arthur P.H.
e1bfa8f6-243c-44db-85c6-94361cb15592
Jung, Hwajin
6f57b703-4c57-4178-a819-b8cd222abcbc
Kohansalnodehi, Mahdokht
f7bc5aae-2fc0-495e-9858-96bb99226946
Kramarz, Barbara
23b48662-a87a-46ab-832c-a92ac26f2c36
Lipstein, Noa
5c57a6dc-eb89-4bfc-92ba-b9e300fa6cf4
Lovering, Ruth C.
7b57a352-c712-4d27-9193-9030016794c9
MacGillavry, Harold
badcfbc0-f9fa-4a5d-bafc-c3b7f1c2bcf6
Mariano, Vittoria
819fbb21-8660-40ea-953e-c306423902f3
Mi, Huaiyu
bd7ffa6f-f686-45ec-b715-164400103b1b
Ninov, Momchil
3aae2945-00b3-4275-bcce-7f0ce033d33d
Osumi-Sutherland, David
0a2240d0-2a7e-4dd3-9025-db223f33925a
Pielot, Rainer
a93d9549-ba00-401f-bf05-049bf07daca9
Smalla, Karl Heinz
a3a4fc38-8e08-42b4-b7b3-2e89edb44ad8
Tang, Haiming
091c57a9-f111-42cd-b2b3-3a2b4ff8e529
Tashman, Katherine
27854236-7fd4-433d-945f-90de0132b379
Toonen, Ruud F.G.
f0f56697-3bd2-43ca-baaf-917ca8cc55eb
Verpelli, Chiara
ce63060e-0f5c-4e8c-9fe4-877e4059e727
Reig-Viader, Rita
3caf0223-6994-41bb-be6e-ca4991df99ff
Watanabe, Kyoko
34e2799b-d308-491d-9efa-332bc850da13
van Weering, Jan
c3bd321b-3164-450c-bbda-7fdc98704f05
Achsel, Tilmann
2617fba9-9fde-4bd6-95af-6ddda258fa08
Ashrafi, Ghazaleh
11d09efa-db96-4c34-aef2-6896ec578330
Asi, Nimra
e639e152-b5cf-44f0-8e72-96fe7113a30a
Brown, Tyler C.
19f49319-ac8c-4b3d-801b-f4dbe0e6e6a4
De Camilli, Pietro
21b07095-0faa-42d0-af59-e769b5743612
Feuermann, Marc
67f253d3-3f49-4249-9ea8-60e63a392121
Foulger, Rebecca E.
ab5bb433-6518-4b1d-88d7-6279305e5765
Gaudet, Pascale
e06a5382-3db3-45be-815a-c1c9bf52dabf
Joglekar, Anoushka
f6bec95a-870b-4367-8700-05fa67dec46f
Kanellopoulos, Alexandros
90fbf183-9cd6-4ded-a1ae-5077587e3dea
Malenka, Robert
ad7a704b-848a-44b8-a1e2-6ddefc365234
Nicoll, Roger A.
95d2d9c8-7db2-45cb-a04c-220e27165799
Pulido, Camila
790f9fa3-1e24-407c-bd4d-348b2b483444
de Juan-Sanz, Jaime
ec528723-f5e5-4983-91cd-383c074f4a67
Sheng, Morgan
a67552b5-362a-415c-b3ae-b3a87a15c6f8
Südhof, Thomas C.
172ec4da-ad42-4b1f-bd99-6b7d288e040c
Tilgner, Hagen
1b6ac6b8-fa2e-473e-9fd3-f52822764100
Bagni, Claudia
b29d9dcf-4d13-462b-9e2f-4bc69a01758e
Bayes, Alex
d64dd544-d1ea-4273-b308-18f0dd28e5bc
Biederer, Thomas
82cbbe00-12fb-41dd-a32b-0286cc53bc65
Brose, Nils
d04f5e22-663a-4aac-a658-0277247ed6f9
En Chua, John Jia
8c18e415-dc3f-4bf1-8a9f-6e2b1374d182
Dieterich, Daniela C.
f04c9003-eb7e-42af-aa9f-a82ecde9999a
Gundelfinger, Eckart D.
9df63bb1-fb57-4c43-a1d3-e019ddfb2a2c
Hoogenraad, Casper
02ca20f1-5bae-4e33-a56f-54f7eefed4e5
Huganir, Richard
02e050bf-58ee-4108-ac04-f9c84f6056b4
Jahn, Reinhard
b0898149-5f4a-4b63-8459-e338e0892726
Kaeser, Pascal S.
fb8aa4f2-d850-4793-a48c-a34e1159ec14
Kim, Eunjoon
0aea376a-f569-4199-961a-1709cc98799e
Kreutz, Michael R.
8f0678fd-10e6-4638-9c59-3954ba3ea57f
McPherson, Peter S.
e5101fdd-1ca4-4864-b603-5ea0a2363f11
Neale, Ben M.
e7761c17-a819-4433-b849-2d977af57ecc
O'Connor, Vincent
8021b06c-01a0-4925-9dde-a61c8fe278ca
Posthuma, Danielle
bff771d6-3fd5-422f-8664-7ba35d79b32f
Ryan, Timothy A.
7a9e4b15-e7ae-4283-8a4a-da94b0bed2c4
Sala, Carlo
889c3543-1a1a-434b-bfd9-a5781bf0b3c0
Feng, Guoping
b105c70c-5a34-46cf-b606-40289a0e0580
Hyman, Steven E.
0ec9255b-ec24-4621-b06a-3e40164ddfd9
Thomas, Paul D.
54f49644-9ea0-4652-ae3f-ffd3e47cf009
Smit, August B.
31968f76-81f2-4560-b5b7-17d8b6925c33
Verhage, Matthijs
f2807ae7-91bb-4331-84c9-7abbd9cdd73e
Koopmans, Frank
ad55cb7b-0d2a-4fb2-9979-39fef93cfbab
van Nierop, Pim
39ec73cc-0f66-4408-a3a3-ea5adc40d258
Andres-Alonso, Maria
f39dfd55-bb9d-4f9e-9290-161dbbc2c3a2
Byrnes, Andrea
63034b4f-cd0c-4cc4-9103-0177ed3f5a75
Cijsouw, Tony
d53f782a-5249-4d9d-acf4-b91acf9418ed
Coba, Marcelo P.
b2c97251-abe6-46f0-98d4-86d8b2dae2b4
Cornelisse, L. Niels
75489a0b-1a34-4efa-9321-8ea4bb631679
Farrell, Ryan J.
2d6aabca-4aa2-48d1-bfb7-66accb790157
Goldschmidt, Hana L.
1101d02f-86e3-4d05-8d4e-0d5391ab946f
Howrigan, Daniel P.
cb4cafba-d5be-4d48-9f6b-d2a0a795418d
Hussain, Natasha K.
06f25c3c-6481-48de-bc4e-6c677198c20e
Imig, Cordelia
7029499e-53a2-482c-964c-40b17ec920bb
de Jong, Arthur P.H.
e1bfa8f6-243c-44db-85c6-94361cb15592
Jung, Hwajin
6f57b703-4c57-4178-a819-b8cd222abcbc
Kohansalnodehi, Mahdokht
f7bc5aae-2fc0-495e-9858-96bb99226946
Kramarz, Barbara
23b48662-a87a-46ab-832c-a92ac26f2c36
Lipstein, Noa
5c57a6dc-eb89-4bfc-92ba-b9e300fa6cf4
Lovering, Ruth C.
7b57a352-c712-4d27-9193-9030016794c9
MacGillavry, Harold
badcfbc0-f9fa-4a5d-bafc-c3b7f1c2bcf6
Mariano, Vittoria
819fbb21-8660-40ea-953e-c306423902f3
Mi, Huaiyu
bd7ffa6f-f686-45ec-b715-164400103b1b
Ninov, Momchil
3aae2945-00b3-4275-bcce-7f0ce033d33d
Osumi-Sutherland, David
0a2240d0-2a7e-4dd3-9025-db223f33925a
Pielot, Rainer
a93d9549-ba00-401f-bf05-049bf07daca9
Smalla, Karl Heinz
a3a4fc38-8e08-42b4-b7b3-2e89edb44ad8
Tang, Haiming
091c57a9-f111-42cd-b2b3-3a2b4ff8e529
Tashman, Katherine
27854236-7fd4-433d-945f-90de0132b379
Toonen, Ruud F.G.
f0f56697-3bd2-43ca-baaf-917ca8cc55eb
Verpelli, Chiara
ce63060e-0f5c-4e8c-9fe4-877e4059e727
Reig-Viader, Rita
3caf0223-6994-41bb-be6e-ca4991df99ff
Watanabe, Kyoko
34e2799b-d308-491d-9efa-332bc850da13
van Weering, Jan
c3bd321b-3164-450c-bbda-7fdc98704f05
Achsel, Tilmann
2617fba9-9fde-4bd6-95af-6ddda258fa08
Ashrafi, Ghazaleh
11d09efa-db96-4c34-aef2-6896ec578330
Asi, Nimra
e639e152-b5cf-44f0-8e72-96fe7113a30a
Brown, Tyler C.
19f49319-ac8c-4b3d-801b-f4dbe0e6e6a4
De Camilli, Pietro
21b07095-0faa-42d0-af59-e769b5743612
Feuermann, Marc
67f253d3-3f49-4249-9ea8-60e63a392121
Foulger, Rebecca E.
ab5bb433-6518-4b1d-88d7-6279305e5765
Gaudet, Pascale
e06a5382-3db3-45be-815a-c1c9bf52dabf
Joglekar, Anoushka
f6bec95a-870b-4367-8700-05fa67dec46f
Kanellopoulos, Alexandros
90fbf183-9cd6-4ded-a1ae-5077587e3dea
Malenka, Robert
ad7a704b-848a-44b8-a1e2-6ddefc365234
Nicoll, Roger A.
95d2d9c8-7db2-45cb-a04c-220e27165799
Pulido, Camila
790f9fa3-1e24-407c-bd4d-348b2b483444
de Juan-Sanz, Jaime
ec528723-f5e5-4983-91cd-383c074f4a67
Sheng, Morgan
a67552b5-362a-415c-b3ae-b3a87a15c6f8
Südhof, Thomas C.
172ec4da-ad42-4b1f-bd99-6b7d288e040c
Tilgner, Hagen
1b6ac6b8-fa2e-473e-9fd3-f52822764100
Bagni, Claudia
b29d9dcf-4d13-462b-9e2f-4bc69a01758e
Bayes, Alex
d64dd544-d1ea-4273-b308-18f0dd28e5bc
Biederer, Thomas
82cbbe00-12fb-41dd-a32b-0286cc53bc65
Brose, Nils
d04f5e22-663a-4aac-a658-0277247ed6f9
En Chua, John Jia
8c18e415-dc3f-4bf1-8a9f-6e2b1374d182
Dieterich, Daniela C.
f04c9003-eb7e-42af-aa9f-a82ecde9999a
Gundelfinger, Eckart D.
9df63bb1-fb57-4c43-a1d3-e019ddfb2a2c
Hoogenraad, Casper
02ca20f1-5bae-4e33-a56f-54f7eefed4e5
Huganir, Richard
02e050bf-58ee-4108-ac04-f9c84f6056b4
Jahn, Reinhard
b0898149-5f4a-4b63-8459-e338e0892726
Kaeser, Pascal S.
fb8aa4f2-d850-4793-a48c-a34e1159ec14
Kim, Eunjoon
0aea376a-f569-4199-961a-1709cc98799e
Kreutz, Michael R.
8f0678fd-10e6-4638-9c59-3954ba3ea57f
McPherson, Peter S.
e5101fdd-1ca4-4864-b603-5ea0a2363f11
Neale, Ben M.
e7761c17-a819-4433-b849-2d977af57ecc
O'Connor, Vincent
8021b06c-01a0-4925-9dde-a61c8fe278ca
Posthuma, Danielle
bff771d6-3fd5-422f-8664-7ba35d79b32f
Ryan, Timothy A.
7a9e4b15-e7ae-4283-8a4a-da94b0bed2c4
Sala, Carlo
889c3543-1a1a-434b-bfd9-a5781bf0b3c0
Feng, Guoping
b105c70c-5a34-46cf-b606-40289a0e0580
Hyman, Steven E.
0ec9255b-ec24-4621-b06a-3e40164ddfd9
Thomas, Paul D.
54f49644-9ea0-4652-ae3f-ffd3e47cf009
Smit, August B.
31968f76-81f2-4560-b5b7-17d8b6925c33
Verhage, Matthijs
f2807ae7-91bb-4331-84c9-7abbd9cdd73e

Koopmans, Frank, van Nierop, Pim, Andres-Alonso, Maria, 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, David, Pielot, Rainer, Smalla, Karl Heinz, Tang, Haiming, Tashman, Katherine, Toonen, Ruud F.G., Verpelli, Chiara, Reig-Viader, Rita, Watanabe, Kyoko, van Weering, Jan, Achsel, Tilmann, Ashrafi, Ghazaleh, Asi, Nimra, 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, Jaime, Sheng, Morgan, Südhof, Thomas C., Tilgner, Hagen, Bagni, Claudia, Bayes, Alex, Biederer, Thomas, Brose, Nils, En Chua, John Jia, Dieterich, Daniela C., Gundelfinger, Eckart D., Hoogenraad, Casper, Huganir, Richard, Jahn, Reinhard, Kaeser, Pascal S., Kim, Eunjoon, Kreutz, Michael R., McPherson, Peter S., Neale, Ben M., O'Connor, Vincent, Posthuma, Danielle, Ryan, Timothy A., Sala, Carlo, Feng, Guoping, Hyman, Steven E., Thomas, Paul D., Smit, August B. and Verhage, Matthijs (2019) SynGO: an evidence-based, expert-curated knowledge base for the synapse. Neuron, 103 (2), 217-234.e4. (doi:10.1016/j.neuron.2019.05.002).

Record type: Article

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.

Text
SynGO_v2 - Accepted Manuscript
Download (331kB)
Text
SynGO_v2 Accepted Manuscript
Restricted to Repository staff only
Request a copy
Text
SynGO_figures - v2
Restricted to Repository staff only
Request a copy

More information

Accepted/In Press date: 30 April 2019
e-pub ahead of print date: 3 June 2019
Published date: 17 July 2019
Keywords: enrichment study, gene annotation, Gene Ontology, gene set analysis, synapse, synaptic plasticity, synaptic proteome network, synaptome, synaptopathies

Identifiers

Local EPrints ID: 433646
URI: http://eprints.soton.ac.uk/id/eprint/433646
ISSN: 0896-6273
PURE UUID: 87ff547d-e48e-4eaa-9ec1-33581404c518

Catalogue record

Date deposited: 28 Aug 2019 16:31
Last modified: 26 Nov 2021 06:59

Export record

Altmetrics

Contributors

Author: Frank Koopmans
Author: Pim van Nierop
Author: Maria Andres-Alonso
Author: Andrea Byrnes
Author: Tony Cijsouw
Author: Marcelo P. Coba
Author: L. Niels Cornelisse
Author: Ryan J. Farrell
Author: Hana L. Goldschmidt
Author: Daniel P. Howrigan
Author: Natasha K. Hussain
Author: Cordelia Imig
Author: Arthur P.H. de Jong
Author: Hwajin Jung
Author: Mahdokht Kohansalnodehi
Author: Barbara Kramarz
Author: Noa Lipstein
Author: Ruth C. Lovering
Author: Harold MacGillavry
Author: Vittoria Mariano
Author: Huaiyu Mi
Author: Momchil Ninov
Author: David Osumi-Sutherland
Author: Rainer Pielot
Author: Karl Heinz Smalla
Author: Haiming Tang
Author: Katherine Tashman
Author: Ruud F.G. Toonen
Author: Chiara Verpelli
Author: Rita Reig-Viader
Author: Kyoko Watanabe
Author: Jan van Weering
Author: Tilmann Achsel
Author: Ghazaleh Ashrafi
Author: Nimra Asi
Author: Tyler C. Brown
Author: Pietro De Camilli
Author: Marc Feuermann
Author: Rebecca E. Foulger
Author: Pascale Gaudet
Author: Anoushka Joglekar
Author: Alexandros Kanellopoulos
Author: Robert Malenka
Author: Roger A. Nicoll
Author: Camila Pulido
Author: Jaime de Juan-Sanz
Author: Morgan Sheng
Author: Thomas C. Südhof
Author: Hagen Tilgner
Author: Claudia Bagni
Author: Alex Bayes
Author: Thomas Biederer
Author: Nils Brose
Author: John Jia En Chua
Author: Daniela C. Dieterich
Author: Eckart D. Gundelfinger
Author: Casper Hoogenraad
Author: Richard Huganir
Author: Reinhard Jahn
Author: Pascal S. Kaeser
Author: Eunjoon Kim
Author: Michael R. Kreutz
Author: Peter S. McPherson
Author: Ben M. Neale
Author: Danielle Posthuma
Author: Timothy A. Ryan
Author: Carlo Sala
Author: Guoping Feng
Author: Steven E. Hyman
Author: Paul D. Thomas
Author: August B. Smit
Author: Matthijs Verhage

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×