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

Colorectal Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by Spring Yingchun Liu (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Association of mutation, copy number alteration, and subtype markers with pathways. Broad Institute of MIT and Harvard. doi:10.7908/C14X56M2

- Overview

+ Introduction

- Summary

There are 35 genes with significant mutation (Q value <= 0.1) and 373 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 246 for subtype 1, 246 for subtype 2, 246 for subtype 3, 246 for subtype 4, 246 for subtype 5, 246 for subtype 6, 246 for subtype 7. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

21 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

0 pathways significantly enriched with marker genes of gene expression subtype 7

- Results

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

Pathway	Nof Genes	Nof CNV_Mut	Enrichment	Q value
KEGG_COLORECTAL_CANCER	62	12	3.3	0
KEGG_PANCREATIC_CANCER	70	11	3	0
KEGG_ENDOMETRIAL_CANCER	52	10	3.3	0
KEGG_PROSTATE_CANCER	89	11	2.7	0.0001
KEGG_PATHWAYS_IN_CANCER	328	20	1.7	0.0004

+ 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

+ The top five pathways enriched with marker genes of gene expression subtype 7

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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