Use of a different DB for ORA enrichment in NTA analysis

[Charline Jnnt]

Hi John, 

These will (normally) be my last questions. 

I am interested in the Network Topolgy-based application provided by WebGestalt tool and was wondering if it was possible to use another pathway database for ORA enrichment (different from Gene Ontology Biological Processes) ?  

In addition, can you explain how the ORA enrichment is calculated in the NTA analysis ? Are the genes of the build selected network used as ReferenceSet for enrichment (instead of genome in a simple ORA enrichment for example)? 

Best,

Charline

[John Elizarraras]

Hello,

For NTA, the only database available is the GO: Biological Process database. If you would like, you could download the results and look at the seedsInNetwork.txt file to get the interesting gene list and independently perform your own ORA analysis.

For the ORA enrichment, you are correct in how the reference set is selected. All of the genes that are in the network make up the reference set, and the identified nodes from the analysis are the interesting list.

If you have any questions, please let me know!

Best,

John

[Charline Jnnt]

Hello, 

For NTA with Network_Retrieval_Prioritization construction , isn't it better to take seedsinSubnetwork.txt file to do the enrichment ourselves? When building network with Expansion_Network parameter, should the combination of candidate.txt and seedsinSubnetwork.txt be taken into account for the enrichment ? 

Of course, we can perform ourselves the enrichment but as the genes of the build selected network are not supplied (we only have access to the number of these genes in the output), the reference set will be different and so will the enrichment...

Best, 

Charline