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 |
|---|---|---|---|
| BCAN(28),ADAMTS4(27),SERPINA3(70),MST1(3) | 4 | 0.041 | 1 |
| KCNJ2(21),ADRB2(40),HTR4(40),AKAP5(70) | 4 | 0.041 | 1 |
| MET(99),ARHGEF12(49),PLXNB1(1),MLL(52) | 4 | 0.041 | 1 |
| RERE(114),TRIP6(98),FBLN1(48),ECM1(28) | 4 | 0.041 | 1 |
| SGCD(40),ADRA1B(40),KCND2(97),FLNC(99) | 4 | 0.041 | 1 |
| CDH9(32),CDH18(32),CDH12(34),CDH10(32),CDH6(31) | 5 | 0.000 | 1 |
| HDAC4(43),CYFIP2(40),FXR1(15),REV3L(51),ATRX(140),LUC7L2(97) | 6 | 0.000 | 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.