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
There are 3 genes with significant mutation (Q value <= 0.1) and 658 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 885 for subtype 1, 885 for subtype 2, 885 for subtype 3. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :
14 pathways significantly enriched with genes with copy number alteration or mutation.
0 pathways significantly enriched with marker genes of gene expression subtype 1
2 pathways significantly enriched with marker genes of gene expression subtype 2
1 pathways significantly enriched with marker genes of gene expression subtype 3
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_PROTEASOME | 48 | 11 | 3 | 0 | 0 |
| BIOCARTA_CHREBP2_PATHWAY | 44 | 9 | 2.8 | 0 | 0.0009 |
| KEGG_WNT_SIGNALING_PATHWAY | 151 | 16 | 1.8 | 0 | 0.0024 |
| BIOCARTA_MTOR_PATHWAY | 23 | 6 | 3 | 0.0001 | 0.0041 |
| KEGG_OOCYTE_MEIOSIS | 114 | 13 | 1.9 | 0.0001 | 0.0041 |
SHFM1,PSMA7,PSMF1,PSMB6,PSMB3,PSMD3,PSMD4,PSMD12,PSMD11,PSMC1,PSME3
PPP2R5D,PPP2R5C,PPP2CB,PPP2R2D,YWHAB,YWHAE,MLX,PPP2R5E,PPP2R2A
PPP2R5D,PPP2R5C,PRKX,CSNK2A1,PPP2R5E,DAAM1,DVL2,SMAD4,SMAD3,TP53,CAMK2G,PPP2CB,PPP3CB,PPP3CC,APC,FZD3
RPS6KB1,FKBP1A,PTEN,EIF4EBP1,EIF6,EIF4A1
PPP2R5D,PPP2R5C,AURKA,PRKX,PPP2R5E,CAMK2G,PPP2CB,PPP3CB,PPP3CC,YWHAB,YWHAE,SMC3,CALM1
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_CELL_ADHESION_MOLECULES_CAMS | 134 | 16 | 1.6 | 0 | 0.016 |
| KEGG_CHEMOKINE_SIGNALING_PATHWAY | 190 | 18 | 1.3 | 0.0004 | 0.022 |
| KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS | 97 | 12 | 1.7 | 0.0004 | 0.022 |
| KEGG_LEISHMANIA_INFECTION | 72 | 10 | 1.8 | 0.0004 | 0.022 |
| KEGG_DILATED_CARDIOMYOPATHY | 92 | 12 | 1.8 | 0.0002 | 0.022 |
PDCD1LG2,HLA-DPA1,ITGB2,PVRL1,ITGAV,HLA-DPB1,ITGA4,HLA-DMB,SDC2,ICAM3,CD86,CDH2,PTPRC,SELP,NLGN2,CLDN23
ADCY2,GNGT2,GNG7,NCF1,CCR6,CCR3,CCR2,CCL2,FGR,CCL7,DOCK2,AKT3,SHC4,PRKCB,GNB4,CCR1,GNG11,CCL21
NCF1,DOCK2,SPHK2,SPHK1,MYO10,AKT3,PRKCB,CFL2,FCGR1A,PTPRC,FCGR2B,FCGR2A
HLA-DMB,NCF2,NCF1,PRKCB,HLA-DPA1,ITGB2,FCGR1A,HLA-DPB1,ITGA4,FCGR2A
ADCY2,ACTG1,DES,SGCD,SGCA,CACNB1,ITGA11,TPM2,ITGAV,IGF1,ITGA4,PLN
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_FOCAL_ADHESION | 201 | 25 | 1.7 | 0 | 0.0001 |
| KEGG_ECM_RECEPTOR_INTERACTION | 84 | 16 | 2.3 | 0 | 0.0001 |
| KEGG_PATHWAYS_IN_CANCER | 328 | 26 | 1 | 0.0005 | 0.06 |
| BIOCARTA_INTRINSIC_PATHWAY | 23 | 5 | 2.4 | 0.0018 | 0.088 |
| KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM | 23 | 5 | 2.4 | 0.0018 | 0.088 |
VEGFB,PDGFRA,PDGFRB,HGF,LAMA4,PARVA,COL6A3,COL6A2,COL6A1,THBS1,THBS4,IGF1,RELN,COL1A1,CAV1,ITGB3,MYL9,ITGAV,ITGA5,AKT3,SHC4,TNC,COL4A4,COL4A2,COL5A1
SDC2,RELN,COL1A1,TNC,ITGB3,ITGAV,COL6A3,COL6A2,COL6A1,THBS1,THBS4,COL4A4,COL4A2,COL5A1,LAMA4,ITGA5
RARA,CCNA1,VEGFB,PDGFRA,PDGFRB,TGFBR1,HGF,LAMA4,NOS2,FGF2,AKR1B1,FZD8,FZD1,IGF1,FOXO1,FGF12,TGFB2,RALA,STK4,FGFR1,ITGAV,TRAF6,E2F2,AKT3,COL4A4,COL4A2
COL4A4,COL4A3,COL4A2,SERPING1,F2R
NMNAT3,ENPP1,NADK,AOX1,NNMT
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_ANTIGEN_PROCESSING_AND_PRESENTATION | 89 | 6 | 3.4 | 0 | 0.0063 |
| BIOCARTA_NKCELLS_PATHWAY | 20 | 3 | 4.4 | 0.0003 | 0.057 |
| KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION | 267 | 7 | 1.9 | 0.0025 | 0.16 |
| KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | 137 | 5 | 2.4 | 0.0023 | 0.16 |
| KEGG_GRAFT_VERSUS_HOST_DISEASE | 42 | 3 | 3.5 | 0.0022 | 0.16 |
KLRC2,KLRC3,CD8A,PSME1,KLRC1,HLA-DRA
KLRC2,KLRC3,KLRC1
FAS,ENC1,CD27,IL15,EDA,CCL4,CXCL13
KLRC2,KLRC3,CD48,FAS,KLRC1
FAS,KLRC1,HLA-DRA
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:
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Enrichment = log2 (# of query genes in the pathway/# No of query genes) - log2 (# of genes in the pathway/# of human genes)
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.
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P value = Fisher exact P value
The Q value is for adjusting P value for multiple testing. A public available R package is used to calculate the Q value.
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.