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

Colon/Rectal Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Spring Yingchun Liu (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Association of mutation, copy number alteration, and subtype markers with pathways. Broad Institute of MIT and Harvard. doi:10.7908/C1Q81B36

- Overview

+ Introduction

- Summary

There are 20 genes with significant mutation (Q value <= 0.1) and 555 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 1960 for subtype 1, 1960 for subtype 2, 1960 for subtype 3, 1960 for subtype 4. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

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

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

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

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

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

- 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	2.8	0
KEGG_PROTEASOME	48	9	2.9	0.0002
KEGG_PANCREATIC_CANCER	70	11	2.5	0.0002
KEGG_ENDOMETRIAL_CANCER	52	10	2.8	0.0002
BIOCARTA_PROTEASOME_PATHWAY	19	6	3.5	0.0005

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

Pathway	Nof Genes	Nof Marker	Enrichment	P value	Q value
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	267	49	1.1	0	0
KEGG_CELL_ADHESION_MOLECULES_CAMS	134	30	1.4	0	0
KEGG_ALLOGRAFT_REJECTION	38	12	2	0	0.0017
KEGG_TYPE_I_DIABETES_MELLITUS	44	12	1.8	0.0001	0.0077
KEGG_HEMATOPOIETIC_CELL_LINEAGE	88	18	1.3	0.0002	0.0096

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

Table 3. Get Full Table Top Pathways enriched with marker genes of gene expression subtype 2 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 2 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 2 in this pathway

Pathway	Nof Genes	Nof Marker	Enrichment	P value	Q value
KEGG_PATHWAYS_IN_CANCER	328	60	1	0	0
BIOCARTA_PPARA_PATHWAY	58	14	1.5	0.0003	0.023
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	267	40	0.77	0.0004	0.023
KEGG_CELL_ADHESION_MOLECULES_CAMS	134	24	1	0.0004	0.023
KEGG_LEISHMANIA_INFECTION	72	16	1.4	0.0003	0.023

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

Pathway	Nof Genes	Nof Marker	Enrichment	P value	Q value
KEGG_GAP_JUNCTION	90	20	1.4	0.0001	0.015
KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION	89	18	1.4	0.0001	0.02
KEGG_CELL_ADHESION_MOLECULES_CAMS	134	24	1.1	0.0003	0.03
BIOCARTA_NO2IL12_PATHWAY	17	6	2	0.0023	0.084
KEGG_LYSOSOME	121	21	0.98	0.0016	0.084

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

Pathway	Nof Genes	Nof Marker	Enrichment	P value	Q value
KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION	44	14	1.8	0	0.002
BIOCARTA_INTEGRIN_PATHWAY	38	12	1.8	0.0001	0.0045
KEGG_CALCIUM_SIGNALING_PATHWAY	178	31	0.98	0.0001	0.0066
BIOCARTA_ECM_PATHWAY	24	8	1.9	0.0007	0.02
BIOCARTA_MCALPAIN_PATHWAY	25	8	1.8	0.001	0.02

+ Methods & Data

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