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 23 genes with significant mutation (Q value <= 0.1) and 255 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.
1 pathways significantly enriched with marker genes of gene expression subtype 1
6 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 |
|---|---|---|---|---|---|
| KEGG_PROTEIN_EXPORT | 24 | 4 | 3.7 | 0.0002 | 0.072 |
| BIOCARTA_AKT_PATHWAY | 22 | 3 | 3.4 | 0.0029 | 0.095 |
| BIOCARTA_CHEMICAL_PATHWAY | 22 | 3 | 3.4 | 0.0029 | 0.095 |
| BIOCARTA_RAS_PATHWAY | 23 | 3 | 3.3 | 0.0033 | 0.095 |
| BIOCARTA_IGF1MTOR_PATHWAY | 20 | 3 | 3.5 | 0.0022 | 0.095 |
SRP54,SEC63,SPCS1,SEC61A1
NFKBIA,CASP9,PIK3CA
CASP9,EIF2S1,PARP1
CASP9,RHOA,PIK3CA
GSK3B,EIF2S1,PIK3CA
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_WNT_PATHWAY | 26 | 10 | 2.1 | 0 | 0.0071 |
| WNT_SIGNALING | 89 | 18 | 1.2 | 0.0006 | 0.059 |
| BIOCARTA_G1_PATHWAY | 28 | 8 | 1.7 | 0.0021 | 0.079 |
| BIOCARTA_P53HYPOXIA_PATHWAY | 22 | 7 | 1.8 | 0.002 | 0.079 |
| KEGG_CELL_CYCLE | 128 | 21 | 0.93 | 0.0024 | 0.079 |
WNT1,CSNK2A1,PPP2CA,FRAT1,MYC,GPI,DVL1,CSNK1D,HDAC1,GSK3B
WNT1,WNT4,CSNK2A1,FRAT1,MYC,CTBP2,FOXN1,TLE2,EP300,WNT11,PPP2CA,GPI,DVL1,FZD6,CSNK1D,GSK3B,SFRP4,LRP5
TGFB3,CDK6,RB1,ATR,CDC25A,ATM,HDAC1,GSK3B
HSP90AA1,FHL2,ABCB1,ATM,RPA1,EP300,CSNK1D
DBF4,TGFB3,CDKN2C,EP300,ANAPC7,TFDP2,ATR,ATM,CDKN1C,HDAC1,MCM7,MYC,CDC7,CCNH,CDK6,RB1,ZBTB17,ORC2L,YWHAE,CDC25A,GSK3B
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_OXIDATIVE_PHOSPHORYLATION | 133 | 31 | 1.6 | 0 | 0 |
| KEGG_CELL_CYCLE | 128 | 25 | 1.2 | 0.0001 | 0.0049 |
| KEGG_PARKINSONS_DISEASE | 130 | 23 | 1.2 | 0.0001 | 0.0049 |
| KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION | 59 | 15 | 1.6 | 0 | 0.0049 |
| KEGG_HEMATOPOIETIC_CELL_LINEAGE | 88 | 19 | 1.4 | 0.0001 | 0.0055 |
NDUFAB1,ATP6V1G3,ATP12A,ATP6V1B1,COX8A,PPA2,UQCRC2,COX11,UQCRFS1,ATP5L,NDUFS3,ATP5H,ATP6V1H,NDUFA10,ATP6V1A,UQCRH,UQCRB,NDUFB5,NDUFB8,ATP6V1G2,NDUFB1,NDUFB2,TCIRG1,NDUFA5,COX7A2,NDUFA8,ATP5F1,NDUFA1,SDHB,SDHD,ATP6V0A4
PTTG2,PTTG1,TGFB1,CCNA2,ESPL1,SKP1,ORC1L,CHEK2,SMAD4,CDC20,CDC26,CDC14B,CDC45L,CDC7,CDC2,MCM4,MCM5,MCM6,BUB1B,BUB1,CDC25C,YWHAE,CDC25B,CCNB2,ORC3L
NDUFAB1,UBA7,COX8A,UQCRC2,UQCRFS1,NDUFS3,ATP5H,SLC25A4,NDUFA10,UQCRH,UBB,UQCRB,NDUFB5,NDUFB8,NDUFB1,NDUFB2,NDUFA5,COX7A2,NDUFA8,ATP5F1,NDUFA1,SDHB,SDHD
OCLN,TLR5,CTNNB1,RHOA,TUBB6,TUBA1A,TUBA1B,TUBB3,LY96,ARPC1B,WASL,EZR,TUBA3C,TUBA3D,CD14
GYPA,CD44,IL4R,CSF3R,CD3G,IL11RA,IL1R2,KIT,ITGAM,CD9,FCGR1A,CD2,CD5,IL6,IL2RA,ITGA3,CD19,ITGA5,CD14
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_WNT_SIGNALING_PATHWAY | 151 | 26 | 0.98 | 0.0004 | 0.039 |
| KEGG_AXON_GUIDANCE | 129 | 23 | 1 | 0.0005 | 0.039 |
| KEGG_COMPLEMENT_AND_COAGULATION_CASCADES | 69 | 16 | 1.4 | 0.0002 | 0.039 |
| KEGG_PATHWAYS_IN_CANCER | 328 | 47 | 0.72 | 0.0003 | 0.039 |
| KEGG_CELL_CYCLE | 128 | 22 | 1 | 0.0008 | 0.054 |
PPP2R5B,BTRC,WNT3A,MMP7,CSNK2A2,WNT1,WNT3,WNT6,ROCK2,EP300,RAC3,CREBBP,PORCN,PRICKLE2,MYC,CTBP2,PRKCG,APC2,TCF7L2,CAMK2B,NFATC3,CSNK2B,FZD6,GSK3B,LRP6,WNT7A
EFNA1,ROCK2,EFNA5,GNAI2,ITGB1,SEMA5B,PTK2,RAC3,MLF2,NTN1,NELL1,CXCR4,PAK4,SEMA3F,SEMA3E,LIMK2,LIMK1,CDK5,SLIT2,SRGAP3,SEMA4D,NFATC3,GSK3B
MASP2,F8,C8G,CNTN1,PROS1,C9,C6,FGA,CR1,CR2,C4BPB,C4BPA,PLG,CD55,SERPIND1,F2R
RARA,RARB,CCNA1,CTNNA2,LAMC3,LAMC1,ITGA2B,RAC3,BMP4,BMP2,MAP2K2,CREBBP,LAMA3,GLI2,NOS2,MYC,CTBP2,APC2,BIRC5,FZD6,RASSF5,GSK3B,WNT7A,PDGFA,WNT3A,WNT1,WNT3,CDKN2B,WNT6,EGFR,EP300,HIF1A,ITGB1,PTK2,EPAS1,E2F1,CYCS,PRKCG,CDK4,TCF7L2,TPM3,MSH6,COL4A2,COL4A1,VHL,MSH2,BAD
TTK,PTTG1,CDC16,CDKN2B,CCNA1,ANAPC5,WEE1,MAD2L1,EP300,ANAPC11,CREBBP,CDC20,CDC26,PLK1,E2F1,MYC,CDK4,MCM4,GADD45G,CDC25C,CCNB2,GSK3B
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.