Translation of homologs (gene.homology)

This module is an interface to NCBI HomoloGene.

orangecontrib.bio.gene.homology.all_genes(taxid)

Return a set of all genes for organism taxid.

orangecontrib.bio.gene.homology.homologs(genename, taxid)

Return a list of homologs (taxid, genename) for a homolog group of gene (organism taxid).

orangecontrib.bio.gene.homology.homolog(genename, taxid, homolotaxid)

Return a homolog of genename (for taxid) in organism holomotaxid. If the homolog does not exist, return None.

orangecontrib.bio.gene.homology.orthologs(genename, taxid, ortholog_taxid=None)

Return all InParanoid orthologs of genename from organism with taxid. If ortholog_taxid is given limit to orthologs from that organism only.

orangecontrib.bio.gene.homology.all_genes_inParanoid(taxid)

Return a set of all genes for organism with taxid in the InParanoid database.

Examples

Mapping homologs from yeast to human:

import orangecontrib.bio.gene
import orangecontrib.bio.taxonomy
import Orange

data = Orange.data.Table("brown-selected")

geneinfo = orangecontrib.bio.gene.NCBIGeneInfo('4932')

genes = [str(ex["gene"]) for ex in data]

for gene in genes:
    mappedgene = orangecontrib.bio.gene.homology.homolog(geneinfo(gene).symbol, \
        '4932', '9606')
    print(gene, mappedgene)