Example: HER2, histone, P28482, P19174-2

How to use PTMcosmos

URL endpoints to a gene and protein directly

Details about a gene at ptmcosmos.wustl.edu/gene/{symbol}/:

Details about an UniProt entry at ptmcosmos.wustl.edu/uniprot/{uniprotac}/:
Ex. P38398

Details about an UniProt isoform at ptmcosmos.wustl.edu/uniprot/isoform/{identifier}/:
Ex. P38398-1

Other useful URL endpoints

Resolve a gene symbol at ptmcosmos.wustl.edu/gene/resolve/{symbol}/:
Ex. All the genes associated with OF, SRC1.


Q: Why is there no information on PTM sites at X gene's page?

PTM site information is stored in each gene's associated UniProt ID page, which can be reached by clicking on the ID. If a gene has multiple protein products, each protein's PTM sites are stored separately.

Q: Why is there little PTM information about non-canonical UniProt isoforms?

We are currently still processing the data for non-canonical UniProt isoforms. These isoforms have much fewer annotations in general.

Q: What is "automatic assertion" evidence?

Evidence tagged as "automatic assertion" means that the experimental procedure was not targeted to that specific type of PTM. For instance, CPTAC uses high-throughput shotgun proteomics, which would fall under this category.

Q: How do you determine the canonical Ensembl transcript for an UniProt isoform?

The longest transcript (excluding introns and UTRs) is considered to be the canonical transcript.

Q: What are the cancer type abbreviations?

In most cases, we use the abbreviations made by TCGA cancer types (studies). For example, UCEC is Uterine Corpus Endometrial Carcinoma and BRCA is Breast Invasive Carcinoma. On top of that, there are some CPTAC conventions different to TCGA's, namely: