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

Glioblastoma Multiforme (Primary solid tumor)

21 April 2013 | analyses__2013_04_21

Maintainer Information

Citation Information

Maintained by Spring Yingchun Liu (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Glioblastoma Multiforme (Primary solid tumor cohort) - 21 April 2013: Association of mutation, copy number alteration, and subtype markers with pathways. Broad Institute of MIT and Harvard. doi:10.7908/C1K0726H

- Overview

+ Introduction

- Summary

There are 66 genes with significant mutation (Q value <= 0.1) and 184 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 2000 for subtype 1, 2000 for subtype 2, 2000 for subtype 3. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

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

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

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

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

- Results

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

Pathway	Nof Genes	Nof CNV_Mut	Enrichment
KEGG_PATHWAYS_IN_CANCER	328	17	2.1
KEGG_GLIOMA	65	11	3.8
KEGG_MELANOMA	71	10	3.6
KEGG_CHRONIC_MYELOID_LEUKEMIA	73	10	3.5
KEGG_NON_SMALL_CELL_LUNG_CANCER	54	8	3.6

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

Table 2. Get Full Table Top Pathways enriched with marker genes of gene expression subtype 1 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 1 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 1 in this pathway

Pathway	Nof Genes	Nof Marker	Enrichment	P value	Q value
KEGG_PATHWAYS_IN_CANCER	328	58	0.96	0	0
KEGG_TYROSINE_METABOLISM	42	14	1.9	0	0.0003
KEGG_MAPK_SIGNALING_PATHWAY	267	46	0.92	0	0.0003
KEGG_HISTIDINE_METABOLISM	29	11	2	0	0.0005
KEGG_CHEMOKINE_SIGNALING_PATHWAY	190	34	0.99	0.0001	0.0009

+ 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	Q value
KEGG_MAPK_SIGNALING_PATHWAY	267	53	1.1	0
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES	69	20	1.7	0
KEGG_PATHWAYS_IN_CANCER	328	68	1.2	0
KEGG_NEUROTROPHIN_SIGNALING_PATHWAY	126	28	1.3	0.0001
KEGG_CHRONIC_MYELOID_LEUKEMIA	73	20	1.6	0.0001

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

Table 4. Get Full Table Top Pathways enriched with marker genes of gene expression subtype 3 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 3 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 3 in this pathway

Pathway	Nof Genes	Nof Marker	Enrichment	P value	Q value
KEGG_CALCIUM_SIGNALING_PATHWAY	178	31	1.1	0.0001	0.0022
KEGG_ENDOCYTOSIS	183	31	1	0.0001	0.0022
KEGG_CELL_ADHESION_MOLECULES_CAMS	134	25	1.2	0.0001	0.0022
KEGG_PATHWAYS_IN_CANCER	328	50	0.86	0	0.0022
BIOCARTA_ACTINY_PATHWAY	20	8	2.2	0.0001	0.0031

+ Methods & Data

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