Kidney Renal Papillary Cell Carcinoma: Clustering of Methylation: consensus NMF<BR>(primary solid tumor cohort)

Kidney Renal Papillary Cell Carcinoma: 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 7833 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 87 samples and 7833 genes identified 3 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-A4-7286-01	1	0.054
TCGA-A4-7585-01	1	0.1
TCGA-A4-7828-01	1	0.22
TCGA-AL-7173-01	1	0.16
TCGA-B1-5398-01	1	0.33
TCGA-BQ-5880-01	1	0.059
TCGA-BQ-5883-01	1	0.2
TCGA-BQ-5884-01	1	0.26
TCGA-BQ-5888-01	1	0.34
TCGA-BQ-5889-01	1	0.41

SampleName	K=2	K=3	K=4	K=5	K=6	K=7	K=8
TCGA-A4-7286-01	1	1	1	1	1	1	1
TCGA-A4-7288-01	1	3	3	3	3	3	3
TCGA-A4-7583-01	1	3	4	1	1	1	1
TCGA-A4-7584-01	1	3	4	4	3	3	3
TCGA-A4-7732-01	1	3	4	4	3	3	3
TCGA-A4-7734-01	1	3	4	4	3	3	5
TCGA-A4-7996-01	1	3	4	1	3	3	3
TCGA-A4-7997-01	1	3	4	1	1	1	1
TCGA-B1-7332-01	1	3	4	1	1	1	1
TCGA-B9-5155-01	1	3	4	1	1	1	3

+ Marker genes of each subtype

Composite.Element.REF	p	difference	q	subclass
ADAMTS1	6.8e-13	0.37	5.4e-10	1
AMACR	1.5e-16	0.35	5.8e-13	1
SNTG2	3.8e-08	0.35	1.9e-06	1
CRYAB	9.3e-14	0.35	1e-10	1
HSPB2	9.3e-14	0.35	1e-10	1
BRSK2	6e-07	0.34	0.000015	1
PDE4D	1.2e-13	0.34	1e-10	1
SLC17A3	6.4e-21	0.33	5e-17	1
ACBD6	9.5e-12	0.33	4.4e-09	1
LYG1	5.7e-11	0.33	1.7e-08	1

+ Methods & Data

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