(WT cohort)
HotNet is an algrithom for finding altered subnetworks in a large protein-protein interaction network conatinning a significant number of mutations and copy number alterations (CNAs).
There were 3 significant subnetworks identified in HotNet analysis.
HotNet identifies 3 altered subnetworks based on the matched somatic mutation and copy number alterations data. Table 1 showes the top 10 significant subnetworks.
Table 1. Get Full Table Top 10 out of 3 subnetworks in ranked by p value. The last column of RepeatTimes shows how many times the subnetwork was picked up in differenct delta values.
| Network | No.ofgenes | p-value | RepeatTimes |
|---|---|---|---|
| PDGFRA(11),PDGFC(10),SHF(11) | 3 | 0.0015 | 1 |
| POLA2(2),MAPK9(8),XPNPEP1(18) | 3 | 0.0015 | 1 |
| UVRAG(1),VPS11(1),VPS18(11) | 3 | 0.0015 | 1 |
Somatic mutation data from Mutsig pipeline, copy number alterations derived from GISTIC pipeline and influence matrix derived from Human Protein Reference Database (HPRD) provided by HotNet website .
HotNet is an algorithm for de novo identification of significantly altered subnetworks.First, it formulates an influence measure between pairs of genes in the network using a diffusion process defined on the graph. Second, it identifies subnetworks using either a combinatorial model or an enhanced influence model. Finally, it derives a two-stage multiple hypothesis test that mitigates the testing of a large number of hypotheses in subnetwork discovery .
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.