How to choose databases to get protein protein interaction data
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2.3 years ago
khsmkal • 0

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 http://interactome.baderlab.org, 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?

Database STRING HuRI Interactome GRI PPI • 692 views
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2.3 years ago

There are plenty of protein-protein interaction databases. Here is a short list:
IntAct
BioGRID (also has genetic interactions)
DIP
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.

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