orange-bioinformatics / docs / reference / obiHomoloGene.htm

Full commit

<title>obiHomoloGene: Translation of homologs</title>
<link rel=stylesheet href="style.css" type="text/css">
<link rel=stylesheet href="style-print.css" type="text/css" media=print>

<h1>obiHomoloGene Translation of homolog genes</h1>
<p>obiHomoloGene is an interface to <a href="">HomoloGene</a>.
<p class=section>Functions</p>
<dl class=attributes>
	<dd>Return a set of all genes with known homologs for organism with <code>taxid</code></dd>
	<dt>homologs(genename, taxid)</dt>
	<dd>Return a list of homologs (homolog_taxid, homolog_genename) for a homolog group that <code>genename, taxid</code> belong to</dd>
	<dt>homolog(genename, taxid, homolotaxid)</dt>
	<dd>Return a homolog of <code>genename, taxid</code> in organism with holomotaxid or None if homolog does not exist.</dd>

<p>Mapping homologs from yeast to human (<a href=""></a>)</p>
<xmp class=code>import orange
import obiHomoloGene, obiTaxonomy, obiGene

data = orange.ExampleTable("../../../../doc/datasets/brown-selected")

geneinfo = obiGene.NCBIGeneInfo('4932')

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

for gene in genes:
    mappedgene = obiHomoloGene.homolog(geneinfo(gene).symbol, '4932', '9606')
    print gene, mappedgene</xmp>
<h1>InParanoid orthologs</h1>
<p>You can also access InParanoid otrhologs database with the <code>orhologs</code> function</p>

<dl class=attributes>
	<dt>homologs(genename, taxid, ortholog_taxid=None)</dt>
	<dd>Return all orthologs of <code>genename</code> from organism with <code>taxid</code>. If <code>ortholog_taxid</code> is given limit to orthologs from that organism only.</dd>
	<dd>Return a set of all genes for organism with <code>taxid</code> in the InParanoid database</dd>