Question: How to choose databases to get protein protein interaction data
gravatar for khsmkal
11 weeks ago by
khsmkal0 wrote:

I have a set of genes associated with a particular complex disease. All the genes are in the HGNC gene symbol format. My aim is to construct a protein interaction directed network in which physical binary interactions are bidirectional and genetic/ functional interactions are unidirectional. Could someone can suggest a database where I can find physical interactions among the given set of genes?. One which I found is HuRI interactome, which doesn't give output for a large set of input genes (there are about 1200 genes in the input gene set). Also, where do I get functional interaction data among these genes? Is the STRING database a good option?

ADD COMMENTlink modified 11 weeks ago by Jean-Karim Heriche18k • written 11 weeks ago by khsmkal0
gravatar for Jean-Karim Heriche
11 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

There are plenty of protein-protein interaction databases. Here is a short list:
BioGRID (also has genetic interactions)
STRING (integrates data from the other databases)

Functional interactions are generally recorded in pathway databases (e.g. Reactome, Panther) or with functional annotations such as with Gene Ontology terms.

ADD COMMENTlink written 11 weeks ago by Jean-Karim Heriche18k
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