Prediction Causative Gene By Network

Question

[Omid]

I have a list of genes related to a disease. Now I would like to apply these Multiple genes and have a network predicting other probable causative genes. I have already applied GENEMANIA and STRING The question is: Is there any other free Network system for prediction?

Answer 1

[Khader Shameer]

GeneMania or STRING is not ideal for inferring diseases associated with a gene list.

You can use one of the following tools/resources for diseases enriched in a disease list:

• Enrichment analysis using Disease Ontology (DO) / DO-Lite. You can Functional Disease Ontology server for enrichment analysis using DO

• DAVID (Expand the Diseases tab and select options. This is mainly for genetic diseases. Default option is OMIM, also available GDA database and GDA class)

• Disease subset of KEGG pathway or Reactome can be inferred using KEGG or Reactome pathway enrichment tools. See this discussion for pathway analysis)

• Other options: Human Phenotype Ontology, GWAS association or any other custom disease-gene annotation/association to perform a standard enrichment analysis. Some of the key aspects of enrichment analysis is discussed here.