Stomach Adenocarcinoma: Clustering of Methylation: consensus NMF<BR>(primary solid tumor cohort)

Stomach Adenocarcinoma: Clustering of Methylation: consensus NMF
(primary solid tumor cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

- Overview

+ Introduction

- Summary

The 6176 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 146 samples and 6176 genes identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

- Results

+ Silhouette width of each sample in robust cluster

+ Gene methylation patterns of molecular subtype

+ Consensus and correlation matrix

+ Samples assignment with silhouette width

SampleName	cluster	silhouetteValue
TCGA-B7-5816-01	1	-0.043
TCGA-BR-6452-01	1	0.29
TCGA-BR-6458-01	1	0.094
TCGA-BR-6566-01	1	0.14
TCGA-BR-7703-01	1	0.32
TCGA-BR-7707-01	1	0.28
TCGA-BR-7717-01	1	0.3
TCGA-BR-7851-01	1	0.21
TCGA-BR-8382-01	1	0.039
TCGA-BR-8487-01	1	0.27

SampleName	K=2	K=3	K=4	K=5	K=6	K=7	K=8
TCGA-B7-5816-01	1	1	1	1	1	1	1
TCGA-B7-5818-01	1	1	2	2	2	2	2
TCGA-BR-6452-01	1	1	1	1	1	1	1
TCGA-BR-6455-01	1	1	2	2	2	2	2
TCGA-BR-6458-01	1	1	1	1	5	5	4
TCGA-BR-6566-01	1	1	1	1	1	1	1
TCGA-BR-6707-01	1	1	2	2	2	2	2
TCGA-BR-6802-01	1	2	3	1	1	1	1
TCGA-BR-6852-01	1	1	2	1	1	1	1
TCGA-BR-7197-01	1	3	4	5	4	4	6

+ Marker genes of each subtype

Composite.Element.REF	p	difference	q	subclass
AUTS2	1.1e-14	0.46	2.1e-13	1
DTX3	1.1e-15	0.45	3e-14	1
CHST10	1.4e-17	0.45	7.5e-16	1
PURG	6.3e-14	0.44	1e-12	1
WRN	6.3e-14	0.44	1e-12	1
ATRNL1	1.3e-13	0.43	1.9e-12	1
SOX5	1.2e-25	0.43	6.3e-22	1
NR3C1	5.4e-14	0.43	8.9e-13	1
RSPO3	2.3e-23	0.43	2.9e-20	1
ST8SIA2	2e-25	0.42	6.3e-22	1

+ Methods & Data

Made with Nozzle