Does ensembl biomart provide ortholog information incomplete?

Question

[Yingzi Zhang]

Deal all, I exported human-pig ortholog relationship information from ensembl biomart. For gene SIRPA, it showed empty information of pig gene/transcrip/protein id nor any ortholog alignment information. But for most other genes, there are such information. So I thought pig doesn't have SIRPA. However, I found pig's SIRPA information when searching the gene in NCBI-gene. Why? I wondered maybe it's because they shared the same gene name but the properties of pig's SIRPA has changed quite a lot from human's SIRPA. But the gene description showed that they are quite the same. Could anyone explain this phenomenon a bit? Does ensembl biomart provide ortholog information incomplete? Thank you.

Best, Yingzi

[Emily]

Please do not send identical messages to Biostars and Ensembl helpdesk. This is known as cross-posting and is bad etiquette as it means more people will try to help you without knowing that you've already been helped. I will close your question on Ensembl helpdesk and answer your query here.

Answer 1

[Emily]

Orthologues in Ensembl are assigned using a protein tree pipeline which clusters proteins sequences using HMMs, then builds multiple alignments and reconciles against the species trees. The relationships between genes in these trees are used to assign homologues.

These are recomputed with each Ensembl release and the pipeline was recently changed from using Blast for the clustering to HMMs, which has altered a lot of trees. The previous version of Ensembl had human/pig orthologues with many-to-many relationships, which has changed. I think this needs to be re-examined and the orthologues restored. I recommend using the archive version of Ensembl for now.

[ForeverFly]

Hi,Emily!I have one question about the change of pipeline.Accoding to your description, did you mean this step has changed?

Run an HMM search on the TreeFam HMM library to classify the sequences into their families.

[Emily]

Yes, that step previously used BLAST.

[Yingzi Zhang]

Apologize for my bad behavior. Thank you for your explanation. I found archive version and found it showed SIRPA ortholog relationship between human and pig. But I found gene TNF showed the same problem I described before-I can found TNF both in human and pig, but the archive version showed human doesn't have ortholog of TNF gene in pigs. Why should this happen ? Thank you in advance.

[Emily]

The current version has orthology between human and pig.

[Yingzi Zhang]

I got it. Thank you, Emily.