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

Brain Lower Grade Glioma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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/C1KD1X58

- Overview

+ Introduction

- Summary

There are 60 genes with significant mutation (Q value <= 0.1) and 325 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, 2000 for subtype 4, 2000 for subtype 5, 2000 for subtype 6, 2000 for subtype 7. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

18 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_PARKINSONS_DISEASE	129	12	2.6	0.0003
KEGG_GLIOMA	65	9	2.9	0.0004
KEGG_HUNTINGTONS_DISEASE	182	13	2.1	0.0017
BIOCARTA_IGF1MTOR_PATHWAY	20	5	3.8	0.0019
KEGG_ENDOMETRIAL_CANCER	52	7	2.9	0.0021

+ 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

Made with Nozzle