Need a fast way to see overlap of gene list with Scoliosis.

Question

[screadore]

Hello everyone,

I'm trying to use a list of 130 genes and see their overlap with Scoliosis. I also want to investigate any Copy Number Variation (CNV) information on these genes.

Additionally, I would like to pull their OMIM #, OMIM Phenotype #, Brief description of associated human phenotype.

If anyone can recommend a fast way of generating all of this I would greatly appreciate it.

Answer 1

[jared.andrews07]

The MyGene API provides most of this info. The OMIM info, NCBI summary, associated GO terms, etc. CNV info is going to take some more work, as that will vary widely by tissue, cell type, disease state, etc, so you'll need a more specific focus there.

[screadore]

Thank you very much. Do you have any suggestions in relation to the CNV aspect?

[jared.andrews07]

Not without much more detail and a more focused question.

[screadore]

Also if you have any examples of the code you have used to do an API pull from them if you could share it with me I'd greatly appreciate it!

[jared.andrews07]

They have a live API page where you can play with the requests and all and it'll show you how to construct them. The docs are also quite good and include many examples. In general, it'll return results in XML or JSON format, so picking a parser for one of those will get you rolling. Or you can use the associated R or python packages.

[screadore]

Thank you so much! Would it allow me to do a whole gene list? Also should I be using /gene/{geneid} in the Annotation section?

[jared.andrews07]

Yes. And for individual genes, yes. For a list of IDs, you can use the POST method. I recommend playing with the API or taking a look at the docs for how to get what you need out of it.