Cancer Cell Metabolism Gene DB

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Bullets030.gifccmGDB includes..
   check002.gif  cell metabolism pathway genes
         - 922 KEGG cell metabolic pathway genes

         - 1,597 REACTOME cell metabolic pathway genes

   check002.gif  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

    check002.gif  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

   check002.gif  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 

   check002.gif  Drug-target interaction networks for cell metabolism genes
        - 4,059 Drugs
        - Drug-gene interaction networks

 

Bullets030.gifccmGDB's finding..

   check002.gif  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


   
check002.gif  Top 50 highly mutated genes in COSMIC data for ccmDB genes

Top 50 highly mutated genes

   check002.gif  Sample count for top 11 genes per tissue type (for COSMIC SNV data)

Sample count for top 11 genes

Sample count for top 11 genes

    check002.gif  # Total ccmDB genes having SNVs in TCGA data

genes having SNVs

genes having SNVs

   check002.gif  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]

Bullets030.gifReferences for Databases
1
Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long
2 Tumor Suppressor gene; http://bioinfo.uth.edu/TSGene/
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php
6 BLCA http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html
   BRCA
http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html
   CLL
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   COAD
http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html
   CRC
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   DLBCL
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   ESO
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   GBM
http://www.sciencedirect.com/science/article/pii/S0092867413012087
   HNSC
https://www.sciencemag.org/content/333/6046/1157
   KIRC
http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html
   LAML
http://www.nejm.org/doi/full/10.1056/NEJMoa1301689
   LUAD
http://www.sciencedirect.com/science/article/pii/S0092867412010227
   LUSC
http://www.nature.com/nature/journal/v489/n7417/full/nature11404.html
   MEL
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   MM
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   OV
http://www.nature.com/nature/journal/v474/n7353/full/nature10166.html
   PRAD
http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html
   UCEC
http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html

7 Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/
Catalogue of Cancer Genes; http://www.ncbi.nlm.nih.gov/pubmed/24881052