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 6 significant subnetworks identified in HotNet analysis.
HotNet identifies 6 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 6 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 |
|---|---|---|---|
| ARHGEF2(23),F11R(23),CGN(24) | 3 | 0.0425 | 1 |
| ROBO1(20),ROBO2(21),SLIT3(16) | 3 | 0.0425 | 1 |
| TBL1XR1(32),HIST2H2BE(23),HIST1H4F(14) | 3 | 0.0425 | 1 |
| UBE3C(10),PSMC2(10),PSMD2(32) | 3 | 0.0425 | 1 |
| LILRB2(7),HLA-B(14),HLA-F(13),B2M(8),KIR3DL1(7),MAGEA1(9) | 6 | 0.0220 | 1 |
| MAML1(15),NOTCH4(14),NOTCH2(24),ADAM10(8),DLL1(12),JAG2(5) | 6 | 0.0220 | 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 .
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.