Association of mutation, copy number alteration, and subtype markers with pathways
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Association of mutation, copy number alteration, and subtype markers with pathways. Broad Institute of MIT and Harvard. doi:10.7908/C18W3CQM
Overview
Introduction

This pipeline maps genes, with mutation or copy number alteration AND this alteration is highly correlated with mRNA expression, to pathways curated in the KEGG and BIOCARTA databases. It identifies pathways significantly enriched with these genes. The pipeline also identifies pathways significantly enriched with marker genes of each expression subtype of cancer.

genes with mutation: identified by the Mutation_Significance pipeline

genes with copy number alteration: identified by the CopyNumber_Gistic2 pipeline

correlation between copy number and mRNA expression: identified by the Correlate_CopyNumber_vs_mRNA pipeline

marker genes and expression subtypes: identified by the mRNAConsensusClustering pipeline

Summary

There are 54 genes with significant mutation (Q value <= 0.1) and 439 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, 2000 for subtype 8, 2000 for subtype 9. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

53 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

0 pathways significantly enriched with marker genes of gene expression subtype 8

0 pathways significantly enriched with marker genes of gene expression subtype 9

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

Table 1.  Get Full Table Top Pathways enriched with genes with copy number alteration or mutation. Nof Genes : No. of genes in this pathway. Nof CNV_Mut : No. of genes with copy number alteration or mutation in this pathway. Enrichment , P value and Q value : See Methods & Data below. CNV_Mut Genes in Pathway: genes with copy number alteration or mutation in this pathway.

Pathway Nof Genes Nof CNV_Mut Enrichment P value Q value
KEGG_GLIOMA 62 10 2.8 0 0.0006
BIOCARTA_CHEMICAL_PATHWAY 22 7 3.8 0 0.0006
BIOCARTA_EIF4_PATHWAY 24 7 3.7 0 0.0006
KEGG_ENDOMETRIAL_CANCER 52 9 2.9 0 0.0008
REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE 55 9 2.9 0 0.0008
List of CNV_Mut genes in this pathway

PRKCA,CALM1,MTOR,MAP2K2,AKT1,KRAS,PTEN,TP53,PIK3CA,PIK3CD

List of CNV_Mut genes in this pathway

CASP9,STAT1,PRKCA,AKT1,TP53,ATM,PARP1

List of CNV_Mut genes in this pathway

PTEN,PRKCA,EIF4G3,AKT1,MTOR,PIK3CA,RPS6KB1

List of CNV_Mut genes in this pathway

CASP9,MAP2K2,AKT1,AXIN2,KRAS,PTEN,TP53,PIK3CA,PIK3CD

List of CNV_Mut genes in this pathway

ATM,PSMB1,PSMB4,PSMC1,PSMD4,PSMD12,RFWD2,TP53,CCNE2

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_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 1 in this pathway

List of marker genes for gene expression subtype 1 in this pathway

List of marker genes for gene expression subtype 1 in this pathway

List of marker genes for gene expression subtype 1 in this pathway

List of marker genes for gene expression subtype 1 in this pathway

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_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 2 in this pathway

List of marker genes for gene expression subtype 2 in this pathway

List of marker genes for gene expression subtype 2 in this pathway

List of marker genes for gene expression subtype 2 in this pathway

List of marker genes for gene expression subtype 2 in this pathway

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_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 3 in this pathway

List of marker genes for gene expression subtype 3 in this pathway

List of marker genes for gene expression subtype 3 in this pathway

List of marker genes for gene expression subtype 3 in this pathway

List of marker genes for gene expression subtype 3 in this pathway

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

Table 5.  Get Full Table Top Pathways enriched with marker genes of gene expression subtype 4 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 4 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 4 in this pathway

Pathway Nof Genes Nof Marker Enrichment P value Q value
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 4 in this pathway

List of marker genes for gene expression subtype 4 in this pathway

List of marker genes for gene expression subtype 4 in this pathway

List of marker genes for gene expression subtype 4 in this pathway

List of marker genes for gene expression subtype 4 in this pathway

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

Table 6.  Get Full Table Top Pathways enriched with marker genes of gene expression subtype 5 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 5 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 5 in this pathway

Pathway Nof Genes Nof Marker Enrichment P value Q value
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 5 in this pathway

List of marker genes for gene expression subtype 5 in this pathway

List of marker genes for gene expression subtype 5 in this pathway

List of marker genes for gene expression subtype 5 in this pathway

List of marker genes for gene expression subtype 5 in this pathway

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

Table 7.  Get Full Table Top Pathways enriched with marker genes of gene expression subtype 6 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 6 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 6 in this pathway

Pathway Nof Genes Nof Marker Enrichment P value Q value
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 6 in this pathway

List of marker genes for gene expression subtype 6 in this pathway

List of marker genes for gene expression subtype 6 in this pathway

List of marker genes for gene expression subtype 6 in this pathway

List of marker genes for gene expression subtype 6 in this pathway

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

Table 8.  Get Full Table Top Pathways enriched with marker genes of gene expression subtype 7 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 7 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 7 in this pathway

Pathway Nof Genes Nof Marker Enrichment P value Q value
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 7 in this pathway

List of marker genes for gene expression subtype 7 in this pathway

List of marker genes for gene expression subtype 7 in this pathway

List of marker genes for gene expression subtype 7 in this pathway

List of marker genes for gene expression subtype 7 in this pathway

The top five pathways enriched with marker genes of gene expression subtype 8

Table 9.  Get Full Table Top Pathways enriched with marker genes of gene expression subtype 8 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 8 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 8 in this pathway

Pathway Nof Genes Nof Marker Enrichment P value Q value
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 8 in this pathway

List of marker genes for gene expression subtype 8 in this pathway

List of marker genes for gene expression subtype 8 in this pathway

List of marker genes for gene expression subtype 8 in this pathway

List of marker genes for gene expression subtype 8 in this pathway

The top five pathways enriched with marker genes of gene expression subtype 9

Table 10.  Get Full Table Top Pathways enriched with marker genes of gene expression subtype 9 . Nof Genes : No. of genes in this pathway. Nof Marker : No. of marker genes of gene expression subtype 9 in this pathway. Enrichment , P value and Q value : See Methods & Data below. Marker Gene in Pathway: markers of gene expression subtype 9 in this pathway

Pathway Nof Genes Nof Marker Enrichment P value Q value
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 62 0 NaN 1 1
KEGG_CITRATE_CYCLE_TCA_CYCLE 31 0 NaN 1 1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 27 0 NaN 1 1
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 28 0 NaN 1 1
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 34 0 NaN 1 1
List of marker genes for gene expression subtype 9 in this pathway

List of marker genes for gene expression subtype 9 in this pathway

List of marker genes for gene expression subtype 9 in this pathway

List of marker genes for gene expression subtype 9 in this pathway

List of marker genes for gene expression subtype 9 in this pathway

Methods & Data
Enrichment

Let genes with copy number alteration or mutation be query genes. Let marker genes of specific identified subtypes be query genes. The Enrichment is calculated as:

  • Enrichment = log2 (# of query genes in the pathway/# No of query genes) - log2 (# of genes in the pathway/# of human genes)

P value

The statistical signficance of the pathways that are enriched with genes with copy number alteration or mutation, and the pathways that are enriched with markers genes of specific identified subtypes is measured by P value.

  • P value = Fisher exact P value

Q value

The Q value is for adjusting P value for multiple testing. A public available R package is used to calculate the Q value.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Qi Zheng, GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis, Nucleic Acids Res. 36(issue suppl 2):W358-W363 (2008)