Any preprocessing for iRefIndex 15.0 used in Hierarchical HotNet?

[Güngör Budak]

Hi,

I can't get the same iRefIndex node and edge counts (as in the paper) with the same version. Did you do any filtering or preprocessing?

Thanks!

[Matthew Reyna]

Hi,

For the paper, we considered genes with HUGO IDs, and we only considered the largest connected subgraph. Please see the supplement of the Hierarchical HotNet paper for details.

Best,

Matt

[Güngör Budak]

Hi Matt,

Thanks. Could you please have a look how I attempt to do it here: https://gist.github.com/gungorbudak/08c7a74c5f0e3692c3cdd2c74e86383a

Perhaps the way I compute largest CC is wrong because I get way more nodes which reduces the number of candidate cancer genes a lot.

Best,

Gungor