Weird GO terms of some genes occurred in annotation

[Prunoideae]

From querying the database, I found that the protein "10090.ENSMUSP00000046177" has a GO term "GO:0048749", which is the "compound eye development", a term for insect eye development.

However, the protein comes from Mus musculus, which should not have such term, and it makes downstream analysis really confusing when seeing a mouse has genes related to such terms enriched...

From looking up in String-DB it seems that the same gene does not have this term.

[Cantalapiedra]

Dear @Prunoideae ,

Thank you for reporting this. It is difficult for me to know whether the original gene is not properly annotated, or if the orthologous group is actually broader than "compound eye development", or if eggNOG-mapper is actually reporting a GO term which is too clade specific and it shouldn't be transferred to other orthologous.

Maybe you can have a clue by checking the diamond alignment stats of your query to the eggNOG-mapper seed ortholog. Is it a close or distant hit?

Best,
Carlos

[Prunoideae]

I think it is because the term is too clade-specific. This gene is in the EggNOG 5.0 database.

I queried the database by the query:

SELECT name, gos
FROM prots WHERE name="10090.ENSMUSP00000046177";

And so the result is:

name,gos
10090.ENSMUSP00000046177,"P|GO:0001654|IMP,P|GO:0006810|IEA,P|GO:0006810|ISO,P|GO:0007275|IMP,P|GO:0007423|IMP,P|GO:0008150|IEA,P|GO:0008150|ISO,P|GO:0008150|IMP,P|GO:0008150|IEA,P|GO:0009987|IEA,P|GO:0030154|IEA,P|GO:0032501|IMP,P|GO:0032502|IMP,P|GO:0032502|IEA,P|GO:0042391|ISO,P|GO:0048058|IMP,P|GO:0048513|IMP,P|GO:0048731|IMP,P|GO:0048749|IMP,P|GO:0048856|IMP,P|GO:0048869|IEA,P|GO:0051179|IEA,P|GO:0051179|ISO,P|GO:0051234|IEA,P|GO:0051234|ISO,P|GO:0055085|IEA,P|GO:0055085|ISO,P|GO:0055085|ISO,P|GO:0065007|ISO,P|GO:0065008|ISO,C|GO:0005575|IDA,C|GO:0005623|IDA,C|GO:0005886|IDA,C|GO:0005887|IDA,C|GO:0016020|IDA,C|GO:0016021|IDA,C|GO:0031224|IDA,C|GO:0031226|IDA,C|GO:0044425|IDA,C|GO:0044459|IDA,C|GO:0044464|IDA,C|GO:0071944|IDA,F|GO:0000166|IEA,F|GO:0003674|IEA,F|GO:0003674|ISO,F|GO:0003674|IEA,F|GO:0003824|IEA,F|GO:0005215|IEA,F|GO:0005215|ISO,F|GO:0005488|IEA,F|GO:0005524|IEA,F|GO:0008144|IEA,F|GO:0015399|IEA,F|GO:0015405|IEA,F|GO:0015562|ISO,F|GO:0016462|IEA,F|GO:0016787|IEA,F|GO:0016817|IEA,F|GO:0016818|IEA,F|GO:0016887|IEA,F|GO:0017076|IEA,F|GO:0017111|IEA,F|GO:0022804|IEA,F|GO:0022857|IEA,F|GO:0022857|ISO,F|GO:0030554|IEA,F|GO:0032553|IEA,F|GO:0032555|IEA,F|GO:0032559|IEA,F|GO:0035639|IEA,F|GO:0036094|IEA,F|GO:0042623|IEA,F|GO:0042626|IEA,F|GO:0043167|IEA,F|GO:0043168|IEA,F|GO:0043492|IEA,F|GO:0097159|IEA,F|GO:0097367|IEA,F|GO:1901265|IEA,F|GO:1901363|IEA"

You can see a "P|GO:0048749|IMP" is there.

[Cantalapiedra]

Dear @Prunoideae ,

Thank you very much for looking into this.

I searched your gene "ENSMUSP00000046177" in eggnog5 (http://eggnog5.embl.de/) to double check. I went to the narrowest OG (ENOG504Q28F from Rodentia), and under "Functional profile" there was this GO and also "compound eye corneal lens development".

Since it is annotated like this in eggNOG 5, I guess that there is little that eggNOG-mapper can do about it.

Best,
Carlos

[Prunoideae]

I think I will filter out these terms manually then. Thank you for your clarification.

[Cantalapiedra]

I will leave the issue open, if you don't mind. Since it is a clear example of an issue with GO term annotation scope.

[Prunoideae]

Ok, no problem.