Synaptic Gene Ontologies

An evidence-based, expert-curated resource for synapse function and gene enrichment studies



Gene search

Query a single gene and view available SynGO annotations

Enter the first letters of a gene symbol, or (part of) a gene name, to see matching SynGO annotated genes. Alternatively, you may copy/paste a human gene ID (ensembl, hgnc, etc.). Examples; DLG4, syntaxin, HGNC:12643, ENSG00000106089.

To perform a search by (first characters of a) gene symbol, at least 2 characters must be provided. If you enter 3+ characters, a 'wildcard search' is also performed against gene names and known synonyms. tip: click the examples to see respective search results

Supported gene IDs:

Your gene list

Explore overrepresented synaptic terms compared to a background set and view available synaptic locations/functions of each gene

Input data that are not human hgnc/ensembl/entrez gene IDs or symbols, first need to be mapped using the ID convert tool
click to load Example 1. 354 proteins highly correlated to core PSD proteins in hippocampal sub-cellular proteomes. Pandya et al. 2017 PMID:28935861.
click to load Example 2. 85 proteins identified by immunoisolation of two synaptic vesicle pools from synaptosomes. Morciano et al. 2005. PMID:16269012.
note how some of the postsynaptically annotated proteins also have presynaptic annotations. Always be mindful of proteins with multiple locations and/or functions when interpreting the overrepresentation analysis.
Only human gene identifiers are supported, if your input data from another species you should use external tools (eg; biomart) to retrieve human orthologs first. In below input, gene identifiers can be separated by whitespace, comma or semicolon. Supported gene IDs:
  • Human gene symbol (genenames.org, official nomenclature symbols, but we try to mix-match synonyms as well)
  • HGNC ID (genenames.org, example: HGNC:11444 )
  • Ensembl human gene ID (example: ENSG00000136854 )
  • Entrez human gene ID (example: entrez:6616 )
If you want to analyse a genelist that doesn't contain any of the supported gene IDs, these must be converted first! For example, if your input list contains uniprot protein accessions (eg; from a proteomics dataset) you may use our ID convert tool to map these to HGNC gene identifiers, which can then be used in this tool.
For more information on available background sets and using custom background sets see this section of the help page.

Interactive ontologies

Visualization of synaptic function and subcellular location models. Explore these models and find genes associated to each SynGO term. eg; show all annotated postsynaptic density (PSD) genes.

open viewer

For advanced users we provide tooling to visualize custom scores per gene, or SynGO ontology term, onto our signature SynGO sunburst figures; open color-coding tool

Downloads

Most use-cases of the SynGO data are available through this website, analyzing your datasets is typically done using online tools provided here. The bulk download ZIP file includes all SynGO ontologies and annotations as both Excel tables and JSON data structures convenient for bioinformatic analysis. The included readme.txt file contains further details.

bulk download SynGO release "20231201" (ZIP archive)

bulk download SynGO release "20210225" (ZIP archive)

bulk download SynGO release "20180731" (ZIP archive)

background geneset "brain" (JSON, compressed with ZIP)

background geneset "brainhigh" (JSON, compressed with ZIP)