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 90 genes with significant mutation (Q value <= 0.1) and 380 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 39 for subtype 1, 39 for subtype 2, 39 for subtype 3. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :
2 pathways significantly enriched with genes with copy number alteration or mutation.
0 pathways significantly enriched with marker genes of gene expression subtype 1
6 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_PARKINSONS_DISEASE | 130 | 12 | 2.3 | 0 | 0.0022 |
| KEGG_RIBOSOME | 87 | 10 | 2.4 | 0 | 0.0036 |
| BIOCARTA_RAS_PATHWAY | 23 | 5 | 3.3 | 0.0001 | 0.014 |
| KEGG_CITRATE_CYCLE_TCA_CYCLE | 32 | 5 | 2.9 | 0.0005 | 0.032 |
| KEGG_PROTEASOME | 48 | 6 | 2.6 | 0.0004 | 0.032 |
UBE2J2,COX6B1,VDAC3,PINK1,UQCRFS1,CASP9,NDUFS3,ATP5J,NDUFA8,PARK7,SDHB,SDHD
RPL19,RPL14,RPL15,RPS15,RPL36,RPL32,RSL24D1,RPL29,MRPL23,RPL21
RAF1,CDC42,CASP9,RHOA,PIK3CA
PDHB,SUCLA2,DLAT,SDHB,SDHD
PSMB1,PSMB3,PSMD2,PSMD3,PSMD7,PSMC3
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_RELA_PATHWAY | 16 | 0 | 0 | 1 | 1 |
| BIOCARTA_NO1_PATHWAY | 31 | 0 | 0 | 1 | 1 |
| BIOCARTA_CSK_PATHWAY | 24 | 0 | 0 | 1 | 1 |
| BIOCARTA_AMI_PATHWAY | 20 | 0 | 0 | 1 | 1 |
| BIOCARTA_ARAP_PATHWAY | 18 | 0 | 0 | 1 | 1 |
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_CELL_CYCLE | 128 | 20 | 2.7 | 0 | 0 |
| KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS | 140 | 13 | 2 | 0 | 0.0029 |
| KEGG_DNA_REPLICATION | 36 | 7 | 2.9 | 0 | 0.003 |
| BIOCARTA_MCM_PATHWAY | 18 | 5 | 3.4 | 0.0001 | 0.0042 |
| KEGG_HOMOLOGOUS_RECOMBINATION | 28 | 6 | 3.1 | 0.0001 | 0.0042 |
DBF4,ORC1L,MAD2L1,CHEK1,CDC20,CDC27,CCNE2,CDC45L,CDC6,CDC2,MCM4,MCM6,CCND3,BUB1B,YWHAZ,ORC2L,BUB3,CDC25C,CDC25A,CCNB2
H2AFZ,H2AFX,HIST1H2AD,HIST2H2AB,CTSG,HIST1H2AB,C7,C3,HIST1H2AG,HIST1H2AE,HIST1H2AI,HIST1H2AH,HIST1H2AL
PRIM1,POLE2,RNASEH2A,MCM4,MCM6,RFC5,DNA2
CDC6,MCM4,ORC1L,MCM6,ORC2L
XRCC2,BLM,SHFM1,ATRX,RAD51,RAD54B
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_ECM_RECEPTOR_INTERACTION | 84 | 9 | 2.6 | 0 | 0.0063 |
| KEGG_FOCAL_ADHESION | 201 | 13 | 1.9 | 0.0001 | 0.01 |
| KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM | 85 | 8 | 2.4 | 0.0001 | 0.013 |
| KEGG_ARGININE_AND_PROLINE_METABOLISM | 54 | 6 | 2.7 | 0.0003 | 0.026 |
| KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION | 59 | 6 | 2.6 | 0.0004 | 0.026 |
COL11A1,LAMC2,COL1A1,COL3A1,COL6A3,COL6A1,SPP1,ITGA2,ITGA5
LAMC2,RAC2,SPP1,COL11A1,FLNC,PARVB,COL3A1,COL6A3,COL6A1,COL1A1,ITGA2,ITGA5,ACTB
PRKAB1,TPM2,TPM4,ACTB,ITGA2,CACNA2D2,CACNA2D4,ITGA5
P4HA2,CXCR4,ALDH1B1,PRODH,ALDH3A2,MAOA
TUBB6,NCK1,ARPC2,TUBA3C,TUBA3D,ACTB
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.