I have a bunch of gene names of Apis mellifera (specifically 194). I used these gene names as an input on STRING database to create a network for Drosophila melanogaster. 54 of those genes were also present in D. melanogaster and I received a second network. Is this a credible method of creating homologous gene network. Or should I use the sequences of the 194 genes and BLAST it to the geneset of the D. melanogaster and do it that way?
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$\begingroup$ Wonder why the negative vote. Its a credible question when you see all these papers saying the same genes are present in different species with the same names. $\endgroup$– The Last WordCommented Aug 5, 2018 at 14:27
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2 Answers
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You could try using BioMart in Ensembl Metazoa. Filter by your list of gene names in honeybee, then get the fly homologues as attributes. The homologues are calculated by sequence comparison and clustering.
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Gene names are not consistent across species. Most of the time genes are automatically annotated and the algorithms try to give names that are similar to their matches in other organisms, but not always. It's also more likely that genes will be automatically named/annotated based on their sequence, and manually named/annotated based on their function.
The further away you get from Homo sapiens & Mus musculus (and maybe Caenorhabditis elegans, Arabidopsis thaliana & Danio rerio), the less likely it is to find consistently named genes.
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$\begingroup$ Given the edits to the question i.e. honey bee input and expecting idential names in fruit fly homologs, I suspect the optimal approach for the OP would be to BLAST the 194 sequences against fly to work out the appropriate fly gene. $\endgroup$ Commented Aug 6, 2018 at 14:15
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$\begingroup$ omabrowser.org/oma/home is useful for finding homologous genes in other organisms, but it looks like it lacks coverage for honey bee. $\endgroup$ Commented Aug 6, 2018 at 14:55