Association of mutation, copy number alteration, and subtype markers with pathways

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by Spring Yingchun Liu (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Association of mutation, copy number alteration, and subtype markers with pathways. Broad Institute of MIT and Harvard. doi:10.7908/C1NV9H97

- Overview

+ Introduction

- Summary

There are 27 genes with significant mutation (Q value <= 0.1) and 405 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 852 for subtype 1, 852 for subtype 2, 852 for subtype 3, 852 for subtype 4, 852 for subtype 5, 852 for subtype 6. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

5 pathways significantly enriched with genes with copy number alteration or mutation.

0 pathways significantly enriched with marker genes of gene expression subtype 1

0 pathways significantly enriched with marker genes of gene expression subtype 2

0 pathways significantly enriched with marker genes of gene expression subtype 3

0 pathways significantly enriched with marker genes of gene expression subtype 4

0 pathways significantly enriched with marker genes of gene expression subtype 5

0 pathways significantly enriched with marker genes of gene expression subtype 6

- Results

+ The top five pathways enriched with genes with copy number alteration or mutation

Pathway	Nof Genes	Nof CNV_Mut	Enrichment	P value	Q value
KEGG_PATHWAYS_IN_CANCER	325	21	1.7	0	0.001
KEGG_ENDOMETRIAL_CANCER	52	8	2.9	0	0.0015
BIOCARTA_IGF1MTOR_PATHWAY	20	5	3.6	0	0.0033
KEGG_NOTCH_SIGNALING_PATHWAY	47	7	2.9	0	0.0033
BIOCARTA_CHEMICAL_PATHWAY	22	5	3.5	0.0001	0.0043

+ The top five pathways enriched with marker genes of gene expression subtype 1

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ The top five pathways enriched with marker genes of gene expression subtype 2

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ The top five pathways enriched with marker genes of gene expression subtype 3

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ The top five pathways enriched with marker genes of gene expression subtype 4

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ The top five pathways enriched with marker genes of gene expression subtype 5

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ The top five pathways enriched with marker genes of gene expression subtype 6

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ Methods & Data

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