Skin Cutaneous Melanoma: HotNet pathway analysis of mutation and copy number data
(metastatic tumor cohort)
Maintained by Hailei Zhang (Broad Institute)

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.

Significant subnetworks

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
Methods & Data

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 Method

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 .

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

[1] HotNet
[2] F. Vandin, E. Upfal, and B.J. Raphael., Algorithms for Detecting Significantly Mutated Pathways in Cancer, Journal of Computational Biology 18(3):507-22 (2011)