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 2 genes with significant mutation (Q value <= 0.1) and 231 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 :
0 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
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 |
|---|---|---|---|---|---|
| BIOCARTA_RACCYCD_PATHWAY | 26 | 4 | 3.8 | 0.0002 | 0.042 |
| KEGG_OOCYTE_MEIOSIS | 114 | 7 | 2.5 | 0.0003 | 0.042 |
| KEGG_MAPK_SIGNALING_PATHWAY | 267 | 10 | 1.8 | 0.0008 | 0.043 |
| KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS | 137 | 7 | 2.2 | 0.0007 | 0.043 |
| KEGG_NEUROTROPHIN_SIGNALING_PATHWAY | 126 | 7 | 2.3 | 0.0005 | 0.043 |
AKT1,CCNE1,RAC1,CHUK
BTRC,CUL1,ANAPC2,PPP2R5E,CCNE1,YWHAQ,CALM3
MAP3K4,KRAS,RAC1,MAP2K4,TP53,GNA12,PPP5C,AKT1,MAX,CHUK
BTRC,CUL1,ANAPC2,UBOX5,UBE2G2,UBE2M,UBE3C
NFKBIB,KRAS,RAC1,AKT1,TP53,YWHAQ,CALM3
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 |
|---|---|---|---|---|---|
| BIOCARTA_AMI_PATHWAY | 20 | 6 | 1.8 | 0.0047 | 0.52 |
| BIOCARTA_INTRINSIC_PATHWAY | 23 | 7 | 1.8 | 0.0021 | 0.52 |
| KEGG_COMPLEMENT_AND_COAGULATION_CASCADES | 69 | 13 | 1.1 | 0.0043 | 0.52 |
| KEGG_RIBOSOME | 87 | 14 | 0.91 | 0.012 | 0.97 |
| BIOCARTA_RELA_PATHWAY | 16 | 0 | 0 | 1 | 1 |
F7,PROC,FGG,FGA,F2,SERPINC1
F11,KNG1,PROC,FGG,FGA,F2,SERPINC1
CD46,CFD,KNG1,F11,F7,PROC,SERPINF2,F2,MBL2,FGG,FGA,SERPINC1,VWF
RPL14,RPS27A,RPS16,RPS17,RPL3L,RPL27A,RPL30,RPS28,RPL6,RPL5,RPL26,RPL23A,RPS7,RPL29
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_ADHERENS_JUNCTION | 75 | 17 | 1.4 | 0.0001 | 0.037 |
| KEGG_RIBOFLAVIN_METABOLISM | 16 | 6 | 2.1 | 0.0015 | 0.17 |
| KEGG_ALZHEIMERS_DISEASE | 167 | 25 | 0.89 | 0.0015 | 0.17 |
| BIOCARTA_MAPK_PATHWAY | 87 | 16 | 1.1 | 0.0027 | 0.22 |
| BIOCARTA_CARM_ER_PATHWAY | 35 | 8 | 1.4 | 0.0068 | 0.32 |
WASF3,VCL,CTNNB1,CTNNA3,PARD3,ERBB2,CDH1,ACP1,TCF7L2,PVRL1,SORBS1,RAC1,YES1,MLLT4,PTPRB,GPI,SNAI1
ENPP3,ACP1,ACPP,MTMR2,MTMR6,PHPT1
COX5A,EIF2AK3,NDUFA4L2,ATP2A3,NDUFV1,CACNA1D,ATP5D,UQCRQ,NDUFS6,CASP9,ADAM10,ERN1,NDUFB9,PPP3R1,ATP5G2,NDUFB1,NDUFB2,NOS1,NDUFA3,NDUFA8,CAPN2,NDUFA1,SDHA,LRP1,SDHD
MEF2A,TGFB2,MAX,MAP3K8,MAP4K3,MAPK4,RIPK1,MAP3K13,MAP3K12,MAP3K3,MAP3K2,RAC1,MAP2K4,RPS6KA3,RPS6KA4,MAPK13
TBP,GTF2A1,NR0B1,HIST2H3C,HDAC4,PHB2,CARM1,HDAC6
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_MATURITY_ONSET_DIABETES_OF_THE_YOUNG | 25 | 9 | 2 | 0.0001 | 0.029 |
| KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION | 272 | 40 | 0.77 | 0.0003 | 0.04 |
| KEGG_GLYCEROLIPID_METABOLISM | 49 | 12 | 1.5 | 0.0006 | 0.047 |
| BIOCARTA_CERAMIDE_PATHWAY | 22 | 7 | 1.9 | 0.0017 | 0.093 |
| KEGG_PRION_DISEASES | 35 | 9 | 1.6 | 0.002 | 0.093 |
ONECUT1,PAX4,BHLHA15,SLC2A2,HES1,HHEX,GCK,HNF4A,PKLR
GRIN2D,HTR4,LPAR6,HTR6,PTH2R,GH2,CHRNB4,UTS2R,GLRA3,KISS1R,NMUR1,GHR,GRM5,GRIA3,GRIA1,GABRB2,GRIK3,GABRB1,GHRHR,GALR1,GALR3,NTSR2,DRD1,CNR1,GABRP,GABRD,GRIN1,P2RX4,P2RX1,P2RX2,TACR1,GABBR1,CALCRL,PTGER1,PTGER2,PTGER4,FSHR,CHRM3,CTSG,CALCR
DAK,LCLAT1,GALK2,DGKB,DGKQ,AWAT2,GLA,MBOAT1,MBOAT2,DGKZ,GCK,LIPC
MAP2K1,MAP2K4,NFKB1,FADD,BAD,TNFRSF1A,BAX
ELK1,HSPA1A,IL1A,MAP2K1,SOD1,C8B,NOTCH1,FYN,BAX
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)
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
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.