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
doi:10.7908/C1K0726H
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

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 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

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_PATHWAYS_IN_CANCER 328 17 2.1 0 0
KEGG_GLIOMA 65 11 3.8 0 0
KEGG_MELANOMA 71 10 3.6 0 0
KEGG_CHRONIC_MYELOID_LEUKEMIA 73 10 3.5 0 0
KEGG_NON_SMALL_CELL_LUNG_CANCER 54 8 3.6 0 0
List of CNV_Mut genes in this pathway

HRAS,PDGFRA,TGFA,TGFB3,WNT2,CDKN2A,HIF1A,MET,HDAC2,AKT1,MAX,AKT3,HSP90AA1,RB1,CDK4,MDM2,PIK3R1

List of CNV_Mut genes in this pathway

HRAS,AKT1,CDKN2A,TGFA,AKT3,RB1,CDK4,PDGFRA,MDM2,PIK3R1,CALM1

List of CNV_Mut genes in this pathway

HRAS,AKT1,CDKN2A,AKT3,RB1,CDK4,PDGFRA,MDM2,PIK3R1,MET

List of CNV_Mut genes in this pathway

HRAS,TGFB3,AKT1,CDKN2A,AKT3,RB1,CDK4,MDM2,PIK3R1,HDAC2

List of CNV_Mut genes in this pathway

HRAS,AKT1,CDKN2A,TGFA,AKT3,RB1,CDK4,PIK3R1

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

PGF,BRAF,RXRA,CTNNA1,MAPK3,RAC1,BMP4,SMAD4,SMAD3,SMAD2,CBLC,LAMA4,LAMA5,ETS1,FGF5,FGF7,PTEN,CCNE2,CCNE1,FZD2,STAT1,RASSF1,FGF18,PDGFA,TGFB2,WNT4,SLC2A1,RET,FGF23,FGF22,EP300,FGFR2,WNT5B,AXIN1,EPAS1,HDAC2,E2F1,E2F3,FASLG,AKT1,MAX,PAX8,RHOA,HSP90AA1,PRKCB,DAPK1,WNT11,GSTP1,CKS1B,WNT16,TPM3,FIGF,COL4A2,COL4A1,FLT3,CBL,WNT2B,FZD10

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

TYRP1,ADH1C,WBSCR22,ADH1B,ADH1A,ADH7,AMH,ALDH3A1,DCT,GOT2,HYAL1,HGD,ALDH3B2,TRMT11

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

PRKX,BRAF,MAPK3,CACNB2,RAC1,NTF3,TAOK2,MAP2K4,JMJD7-PLA2G4B,FGF5,FGF7,FLNC,PLA2G3,MAP3K11,GNG12,PPP3CB,CHP,RASA2,DUSP4,MAPK12,FGF18,PDGFA,GNA12,TGFB2,FGF23,FGF22,MAP4K4,ARRB2,NGF,FGFR2,FGFR4,MAP4K2,ELK4,CACNA2D1,CACNA2D2,RAP1A,CACNA1F,CACNA1C,CACNA1A,FASLG,AKT1,MAX,PRKCB,PPM1A,PPP3R1,MAP3K3

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

WBSCR22,ALDH3A1,ASPA,HNMT,HDC,ALDH3B2,ABP1,ALDH7A1,TRMT11,ALDH1B1,ALDH2

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

CXCL11,PRKX,TIAM1,GNG5,ROCK1,BRAF,CCR8,CCR6,ARRB2,CCR4,CCR3,MAPK3,CX3CR1,GNAI3,CCL4,RAC1,RAP1A,XCL1,CXCR3,AKT1,PLCB4,RHOA,PRKCB,GNB5,WASL,PF4,GNG11,GNG12,CCL21,CCL19,STAT1,CCL16,GSK3A,JAK2

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_MAPK_SIGNALING_PATHWAY 267 53 1.1 0 0
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 69 20 1.7 0 0
KEGG_PATHWAYS_IN_CANCER 328 68 1.2 0 0
KEGG_NEUROTROPHIN_SIGNALING_PATHWAY 126 28 1.3 0 0.0001
KEGG_CHRONIC_MYELOID_LEUKEMIA 73 20 1.6 0 0.0001
List of marker genes for gene expression subtype 2 in this pathway

MAP3K4,PLA2G1B,MAP2K5,MECOM,MAPK8,PLA2G2D,CACNB4,HSPA1L,NTF3,MAP2K2,FGF5,FGF7,FGF9,NFKB1,NFKB2,CACNG2,GADD45G,PLA2G3,GADD45B,MAP3K14,MKNK2,PPP3CA,RASA1,PLA2G10,GPI,MAPK11,RPS6KA5,NRAS,RPS6KA6,DUSP2,RPS6KA2,MAPK14,DUSP9,FGF18,FGF17,TGFB3,TGFB2,PRKACB,FGF20,NGF,FGFR4,MAPKAPK2,ELK4,EGF,NR4A1,RAP1A,CACNA1C,PRKCA,PPM1A,PPM1B,MAP3K1,NF1,CRK

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

MASP1,SERPINA5,CD46,CFI,F12,F10,F7,CNTN1,F2,C7,C6,BDKRB1,C1S,FGG,FGA,FGB,CR2,VWF,CPB2,PLAU

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

STAT5B,RARB,CTNNA1,MECOM,CTNNA3,CTNNA2,VEGFB,JUP,PIAS3,MAPK8,BCL2L1,DVL2,MAP2K2,CREBBP,SMAD3,DVL1,CBLC,FGF5,FGF7,FGF9,NFKB1,NFKB2,CTBP1,CTBP2,BIRC5,FZD4,NRAS,TCEB2,TCEB1,WNT7A,FGF18,MMP9,FGF17,TGFB3,MMP2,TGFB2,WNT4,CDKN2B,RALA,FGF20,RBX1,ARNT,ITGAV,EGF,RUNX1,TRAF4,AXIN1,EPAS1,ITGA2,CDKN1A,CDKN1B,ITGA6,ABL1,E2F1,PAX8,TPR,PRKCA,RUNX1T1,DAPK3,WNT11,EGLN2,EGLN1,CDH1,TCF7L1,PIK3R3,CEBPA,COL4A2,CRK

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

FOXO3,NGFRAP1,MAP2K5,RIPK2,MAPK8,NGF,MAPKAPK2,NTF3,MAP2K2,RAP1A,ABL1,NFKB1,CSK,SHC3,KIDINS220,PSEN1,NGFR,MAP3K1,CALML5,PIK3R3,MAPK11,YWHAE,RPS6KA5,RPS6KA6,NRAS,RPS6KA2,MAPK14,CRK

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

E2F1,STAT5B,TGFB3,NFKB1,TGFB2,SHC3,CTBP1,CTBP2,MECOM,BCL2L1,PIK3R3,RUNX1,MAP2K2,SMAD3,CBLC,NRAS,CDKN1A,CDKN1B,ABL1,CRK

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

ADCY8,ITPKB,ITPKA,ATP2B1,ATP2B3,GRIN2C,BST1,NTSR1,PHKA2,ADORA2B,BDKRB1,SPHK1,VDAC2,VDAC3,VDAC1,ATP2A2,TBXA2R,CACNA1G,ADRA1D,EDNRB,PLCB3,PLCB2,PRKCA,GRM1,GNAL,PTAFR,PPP3R1,PTK2B,CHP,CAMK2A,HTR2B

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

CHMP5,CHMP6,DAB2,PLD1,SH3GL1,ASAP2,ADRBK2,SRC,HSPA1L,SNF8,MET,KDR,CBLB,RABEP1,GRK6,CLTB,RAB5B,VPS37A,VPS37B,VPS37C,PIP5K1A,LDLRAP1,RAB11FIP5,RAB11FIP2,RAB11FIP3,EEA1,PIKFYVE,EHD1,FLT1,VPS28,ARAP1

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

OCLN,HLA-DQA1,PHOX2A,HLA-DRA,HLA-DRB1,ITGAV,ITGB7,CTLA4,HLA-DOA,HLA-DOB,CLDN8,CLDN3,CLDN5,HLA-DMB,CD80,CLDN1,VCAN,JAM3,CLDN10,CLDN11,NEO1,CD4,SELPLG,MPZ,SELE

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

CUL2,RARB,CCNA1,PLD1,BCR,RXRA,RXRG,LAMC3,PIAS3,MAPK8,LAMC2,PIAS1,RAC3,DVL3,HGF,LAMA4,CBLB,FGF7,SPI1,MLH1,PTEN,AKR1B1,RAD51,BID,BIRC5,BIRC2,WNT7B,RASSF1,MMP9,CDKN2A,RALA,EP300,RBX1,ITGAV,TRAF4,TRAF3,MET,IKBKG,E2F1,AKT1,FOS,PAX8,PRKCA,NCOA4,WNT16,KITLG,EGLN1,TCF7L2,PIK3R5,RALGDS

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

ABI2,ARPC4,PSMA7,ACTR3,ACTR2,ARPC2,NCK1,PIR

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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)
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