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Database (R or Python) API search for Genes Associated to Phenotype
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5.2 years ago
pietjones • 10
South Africa

Hi,

I have a rather large list of phenotypes (disease names), and I wish to search for genes that are associated with these phenotypes. Is there some API (either Python or R) that can be used to search, for example Ensembl w.r.t hg19, for these disease names and obtain the associated genes? I know I can type the disease manually into Ensembl's search and obtain a list of links, with some naming the particular gene, but I would like to know if there is some automated way to do this. A lot of information online is concerned with doing the reverse, mining for phenotypes associated to a set of genes.

Thanks for any advice :)

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2.8 years ago
Earendil • 20
Sweden

Have you given a try to Phenotype-Genotype Integrator (PheGenI) from dbGaP?

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Thanks for the suggestion, I just tried it, but no results were returned. The searches I tried were: "Propionic acidemia", "Isovaleric acidemia" and "Beta-Ketothiolase deficiency", though searching them directly in Ensembl did return: PCCB, IVD and ACAT1, respectively.

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