Database with gene family annotations

Question

[kjs22]

Hello,

I have a list of genes, and I am looking for a database which will provide me with general gene family annotations, such as whether a gene is a cytokine, chemokine, ribosomal, etc. I've queried the Panther database, but unfortunately it does not return annotations for all of my genes. BiomaRT and ensembldb also provide gene biotype information, but they are more vague than what I am looking for (protein coding, lncRNA, etc). Does anyone have any suggestions for other databases which will have this information?

Thank you so much!

[GenoMax]

What organism are you interested in?

If this is for human, then GeneCards has a lot of information available. An example gene.

Answer 1

[Mensur Dlakic]

I've queried the Panther database, but unfortunately it does not return annotations for all of my genes.

For any reasonably-sized query, it is likely that annotations will not be possible for at least some genes/proteins. That is not a database deficiency - we can't annotate all proteins because there isn't enough information about their functions.

These two databases are fairly general and include almost all known protein families:

• https://www.ebi.ac.uk/interpro/
• https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Their annotation still may not be as neat as you expect, as many proteins have multiple domains and can perform multiple functions.