(primary solid 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 30 significant subnetworks identified in HotNet analysis.
HotNet identifies 30 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 30 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 |
|---|---|---|---|
| ARID1B(156),SMARCA2(166),PRPF6(216) | 3 | 0.0015 | 3 |
| GPR77(57),C5AR1(58),WAS(97) | 3 | 0.0015 | 3 |
| MAP2K4(1),MAP3K4(156),DIXDC1(1) | 3 | 0.0015 | 3 |
| MTTP(100),APOB(11),PDIA4(155) | 3 | 0.0015 | 3 |
| PGM5(1),SNTG2(1),DMD(164) | 3 | 0.0015 | 3 |
| TRIP13(176),LOXL4(3),SEMA4G(1) | 3 | 0.0015 | 3 |
| PDCD11(2),NFRKB(2),NFKB1(100) | 3 | 0.0015 | 2 |
| CACNA1C(169),RYR2(181),ALB(58),CRYAA(1) | 4 | 0.0170 | 2 |
| GRIN2D(59),PPP2R2A(89),INA(1),NF1(147) | 4 | 0.0170 | 2 |
| CASP7(1),KCNJ1(3),GOLGA3(179),CASP2(154) | 4 | 0.0200 | 2 |
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.