I am working with snRNA-seq data and would like advice on best practices for downstream processing of pig gene identifiers and cross-species orthology mappings. I currently use the Ensembl pig gene IDs that are mapped to gene symbols for pig genes. However, many pig genes have no pig symbol, even though Ensembl identifies a human orthologue.
For example:
Pig Ensembl ID: ENSSSCG00000021155
Pig external name: NA
Human orthologue: POMC
Orthology type: one-to-one
orthology_confidence : 1
mapped_to_human: False
orthology_type: ortholog_one2many
I would appreciate advice on the the best practices here :
1: Should I use human gene symbols for my pig analysis irrespective if pig symbols are available or not? Is there a risk that the same gene has different official symbols in pig and humans?
2: If a pig Ensembl gene has no pig symbol but has a high-confidence human orthologue but varying orthology type, what should be the approach towards using the human symbol or using ENSG id ?
3: For downstream processing, should orthology conversion be performed before or after differential expression and marker analysis?
4: When converting results to human orthologues, how should duplicate mappings be handled? For example, if multiple pig genes map to the same human gene, should their statistics be combined, should only the best-supported mapping be retained, or should the genes remain separate?
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Arindam •
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First I should ask what it is you want to do with the data? I'm thinking that you might do differential expression and pathway enrichment? Assuming that is the case, there are strengths and weaknesses for using pig or human IDs. It is more correct to use pig IDs because these better represent the genes that were actually measured, The drawback with this is that they are just IDs and it is hard to interpret ENSG numbers as a biologist. This is why it might be good to include the human ortholog gene symbol, but as you say for many genes there is not a 1-to-1 relationship, so it is not a scientifically correct approach. What I would suggest in your case is to create a gene identifier composed of the pig ENSG ID and the closest human ortholog gene symbol combined -- that way you have the correctness of using the exact ENSG ID that was detected and the ability to interpret the function of the genes at a glance with the human gene symbol. There will be cases where there is a 2-to-1 relationship, which is still fine for this purpose if each pig gene is just included once with its closes human ortholog gene symbol. In the cases where the pig gene has no human homolog, the gene symbol could be left as NA.