Hub genes validation using bioinformatics approach

Question

[s.awasthy]

Hello all, I am working on Gallbladder cancer data (RNASeq). After reading through many papers, GEPIA and UALCAN are used for validation of hub genes. This cancer data is under controlled access (TCGA) and also not mentioned in these two above portals. Please suggest how can i proceed further?

Answer 1

[Michael]

Well, as with all computational predictions, I doubt a "validation" of hub genes can be done properly without experimental data. Also, a definition of the validity of hub identification is required. If you are looking for essential genes or predictive markers, as is common, there is the DepMap Portal, see this example: https://depmap.org/portal/gene/RAB1A?tab=overview

Thus, your validation method could be a database search for functional studies involving those hub genes, be it loss of function or gain of function, mutations, and whether these result in a clear phenotype. Following from such a definition, a good set of hub genes would then have a high probability of being essential in genome-wide assays.