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 7 significant subnetworks identified in HotNet analysis.
HotNet identifies 7 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 7 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 |
|---|---|---|---|
| C19orf57(7),RUNX1T1(5),VCL(10) | 3 | 0.028 | 1 |
| EPHA4(10),NGEF(10),ARHGEF15(5) | 3 | 0.028 | 1 |
| PTEN(10),CTNND2(5),MAGI2(1) | 3 | 0.028 | 1 |
| CUX1(2),SERPINB3(5),ARSA(68),TG(7) | 4 | 0.018 | 1 |
| PHF23(5),RPL18A(6),MAPK8IP2(69),LRSAM1(1) | 4 | 0.018 | 1 |
| PIAS2(5),CHAF1A(6),MBD1(4),GTF2IRD1(2) | 4 | 0.018 | 1 |
| PLXNB2(68),SLC1A6(6),DLG5(12),ABCA1(1) | 4 | 0.018 | 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.