Cancer Cell Metabolism Gene DataBase

Cancer Cell Metabolism Gene DB

Home

ccmGDB includes..
    cell metabolism pathway genes
         - 922 KEGG cell metabolic pathway genes
         - 1,597 REACTOME cell metabolic pathway genes

7 Cancer Gene Source

7 Cancer Gene Source
cf) a; Oncogenes, b; TSGene, c; Cancer Gene Census,d; Cancer Genes, e; Network of Cancer Gene,
f; Siginificantly mutated driver genes, g; Therapeutic Vulnerabilities in Cancer

     Somatic alterations and genetic features for 2,071 cell metabolism genes with efficent visualization
         - 151238 Somatic nucleotide variants (SNVs) data for 41 primary sites (62,599 samples) from COSMIC,
           102399 SNVs for 20 cancer types (5,186 samples) from TCGA
         - 6269 Copy number variation (CNV; 4504 copy number gain, 1784 copy number loss) data
           for 17 primary sites (3,062 samples) from COSMIC
         - 1971 Structural variation (SV) data for 13 primary sites (412 samples) from COSMIC
         - Chitars2.0 - 4,729 chimeric transcripts

    Systematic assessment of transcriptome, protein expression and co-expressed gene network
       over 2,000 cell metabolism genes
        - Differential gene expression (DEG) plots for 8 TCGA cancer types
        - Gene expression in 24 CCLE cancer types
        - Correlation between gene expression and CNV for 15 TCGA cancer types
        - Co-expressed protein interaction network for 8 cancer TCGA types

    Drug-target interaction networks for cell metabolism genes
        - 4,059 Drugs
        - Drug-gene interaction networks

ccmGDB's finding..

Differential gene expressions (t-test, P-value < 0.05)
# DEGs regardless of directionl

	BRCA	COAD	HNSC	KIRC	LUAD	LUSC	THCA	UCEC
ccmGenes	411	366	356	408	403	404	357	335
cmGenes	1752	1534	1488	1734	1694	1755	1533	1405

# DEGs for ccmGenes

ccmGenes	BRCA	COAD	HNSC	KIRC	LUAD	LUSC	THCA	UCEC
Up	180	147	133	188	207	211	146	133
Down	207	141	113	178	148	164	149	107

# DEGs for cmGenes

cmGenes	BRCA	COAD	HNSC	KIRC	LUAD	LUSC	THCA	UCEC
Up	731	493	399	671	865	891	505	492
Down	727	503	460	756	514	615	582	272

Top 50 highly mutated genes in COSMIC data for ccmDB genes

Top 50 highly mutated genes

Sample count for top 11 genes per tissue type (for COSMIC SNV data)

Sample count for top 11 genes

# Total ccmDB genes having SNVs in TCGA data

genes having SNVs

Sample Counts for Top 14 Genes Per Tissue (for TCGA SNV data)

Top 14 Genes Per Tissue
cf) Tissue Abbreviation[Tissue Name]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]