(metastatic tumor 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 5 significant subnetworks identified in HotNet analysis.
HotNet identifies 5 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 5 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 |
|---|---|---|---|
| CDH13(123),ADIPOR2(1),ADIPOQ(23) | 3 | 0.0215 | 1 |
| GSTM1(42),GSTM2(42),GSTM3(44) | 3 | 0.0215 | 1 |
| MTMR7(7),MTMR6(121),MTMR9(2) | 3 | 0.0215 | 1 |
| SLC12A1(98),RELL2(135),RELT(39) | 3 | 0.0215 | 1 |
| UPK3B(3),UPK1B(22),UPK3A(4) | 3 | 0.0215 | 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.