Gene Ontology / Hypothetical proteins

Question

[Pegasus]

Hi all,

I am conducting RNA-seq analysis for a fungal strain (Botrytis cinerea 05.10). Most of the up/down-regulated genes are hypothetical proteins that have no clear function. As I know only those genes with actual names can give a value in the gene ontology and pathway enrichment analysis like go-seq, and KEGG.

I couldn't find these gene_IDs In either the gtf.file or the Ensembl database.

• In such a case, can I use orthologs instead of the actual genes, the function may change among close relative organisms tho.

• Is there any tool that can use the sequences of these proteins/ Ensembl gene-IDs as an input for GO and pathway analysis? Thank you

Answer 1

[Mensur Dlakic]

I was going to suggest this web site:

https://embed.protein.properties/

At the moment it behaves erratically, and not sure when it will be fixed. When it works properly, one enters a protein sequence and it responds by predicting its GO affiliation, along with confidence estimates. That may give you some idea about GO assignments for your proteins if you pick only relatively high-confidence predictions (say, >0.7).

The results from the above website take <10 seconds. If you don't mind waiting a bit longer, this could be useful:

https://predictprotein.org/

If you don't mind installing the program yourself:

https://github.com/Rostlab/goPredSim

[Pegasus]

Thank you so much Dr. Mensur, I will try them