It isn't useful to do enrichment on alleles, phenotype enrichment should be on genes.
Annotations are made to alleles, but alleles are connected to genes, and enrichment of phenotypes is only useful at the gene level.
but for this query template
Genes-> alleles and phenotypes
i) the enrichment ~is~ uses alleles instead of ~phenotypes~ genes
ii) the GO enrichment is missing
For all lists containing gene lists GO and phenotype enrichment should be present.
Enrichment is not required at all for alleles (it would be misleading).
Hi,
It isn't useful to do enrichment on alleles, phenotype enrichment should be on genes. Annotations are made to alleles, but alleles are connected to genes, and enrichment of phenotypes is only useful at the gene level.
I thought this was fixed, and in most cases I think it was by this ticket, https://github.com/intermine/pombemine/issues/30
but for this query template Genes-> alleles and phenotypes i) the enrichment ~is~ uses alleles instead of ~phenotypes~ genes ii) the GO enrichment is missing
For all lists containing gene lists GO and phenotype enrichment should be present. Enrichment is not required at all for alleles (it would be misleading).