Neo4j and Saccharomyces Genome Database

[Jayne Ihaka]

Hi everyone,

Just wondering if this group is still active?

I'm learning how to use Neo4j and Cypher at the moment. I thought I would try combining some results from a synthetic genetic array analysis with data from the Saccharomyces Genome Database and gene ontologies.

I've made my first attempt into a GraphGist and would really appreciate some feedback on it. Finding it a bit of a challenge to clearly articulate why graphs are so useful for this kind of dataset. The link is here.

Has anyone in this group been using data from SGD with Neo4j? If someone can link me to some resources that would be great. I'm currently checking out Bio4j.

Cheers,

Jayne.

[Martin Preusse]

Hi Jayne,

interesting! Your gist looks like you can use it to find GO terms associated to chemical/gene combinations. So you have nicely modeled your data and queried it. Do you have an actual problem or question :) ?

I use GO and other ontologies a lot and I have similar queries for e.g. microRNAs and genes. For me it often works well to consider the neighborhood of the gene. I added gene-gene interactions (e.g. from KEGG or STRING). Then I do an enrichment analysis with the gene + all neighboring genes instead of simply taking all GO terms associated to the gene. The neighboring genes themselves can give you a hint towards the gene's function. Your gene might be a phosphatase, but the target it phosphorylates could be interesting.

Bio4j is huge but maybe a bit overkill if you are getting started.

Cheers
Martin

Am Sonntag, 13. Juli 2014 um 01:24 schrieb Jayne Ihaka:

> Hi everyone,
>
> Just wondering if this group is still active?
>
> I'm learning how to use Neo4j and Cypher at the moment. I thought I would try combining some results from a synthetic genetic array analysis with data from the Saccharomyces Genome Database and gene ontologies.
>

> I've made my first attempt into a GraphGist and would really appreciate some feedback on it. Finding it a bit of a challenge to clearly articulate why graphs are so useful for this kind of dataset. The link is here (http://www.neo4j.org/graphgist?e4f4b46237c68cf8ca68).

>
> Has anyone in this group been using data from SGD with Neo4j? If someone can link me to some resources that would be great. I'm currently checking out Bio4j.
>
> Cheers,
>
> Jayne.
>

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