Missing protein (VEGF-A) in String db

Question

[Phenylananin]

Hello,

my list of proteins that I want to explore in String db contains the vascular endothelial growth factor A (VEGF-A). VEGF-B, -C, and -D can all be found in String, but the human variant of VEGF-A is not included, although it's a well known protein. Am I missing something? Is there the possibility of including VEGF-A from another species in my network of human proteins?

Thanks!

Answer 1

[damian.szk]

We are aware of the issue with VEGFA. Unfortunately, when we froze the human genome VEGFA was marked as pseudogene in Ensembl. As STRING only carries protein-coding genes VEGFA was removed. We can't do much about it in version v12. If the gene is critical to your analysis please continue using version 11.5 which has this gene: https://version-11-5.string-db.org/

[shalespringer]

Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the Ensembl v99 release. It's unfortunate that the Cytoscape app can't use old versions.

I know it's out of your hands for this version, but this may be useful information for future users who find this thread. Querying these missing proteins by gene symbol in Cytoscape currently returns a different protein without notifying the user. Querying VEGFA returns COL18A1 and querying MAPK10 returns DUSP16. The website at least flags these matches for user review but Cytoscape does not. (As always it's just more reliable to use Ensembl or Uniprot ID.)