Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for ADH6
Basic gene info.Gene symbolADH6
Gene namealcohol dehydrogenase 6 (class V)
SynonymsADH-5
CytomapUCSC genome browser: 4q23
Genomic locationchr4 :100125878-100140403
Type of geneprotein-coding
RefGenesNM_000672.3,
NM_001102470.1,
Ensembl idENSG00000172955
Descriptionalcohol dehydrogenase 6aldehyde reductase
Modification date20141207
dbXrefs MIM : 103735
HGNC : HGNC
Ensembl : ENSG00000172955
HPRD : 00067
Vega : OTTHUMG00000131024
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADH6
BioGPS: 130
Gene Expression Atlas: ENSG00000172955
The Human Protein Atlas: ENSG00000172955
PathwayNCI Pathway Interaction Database: ADH6
KEGG: ADH6
REACTOME: ADH6
ConsensusPathDB
Pathway Commons: ADH6
MetabolismMetaCyc: ADH6
HUMANCyc: ADH6
RegulationEnsembl's Regulation: ENSG00000172955
miRBase: chr4 :100,125,878-100,140,403
TargetScan: NM_000672
cisRED: ENSG00000172955
ContextiHOP: ADH6
cancer metabolism search in PubMed: ADH6
UCL Cancer Institute: ADH6
Assigned class in ccmGDBC

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Phenotypic Information for ADH6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADH6
Familial Cancer Database: ADH6
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://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,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_FATTY_ACID_METABOLISM
KEGG_TYROSINE_METABOLISM
KEGG_RETINOL_METABOLISM
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ADH6
MedGen: ADH6 (Human Medical Genetics with Condition)
ClinVar: ADH6
PhenotypeMGI: ADH6 (International Mouse Phenotyping Consortium)
PhenomicDB: ADH6

Mutations for ADH6
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ADH6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=38)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr4:100137326-100137326p.R38C4
chr4:100131365-100131365p.F147F2
chr4:100129959-100129959p.K232E2
chr4:100129871-100129871p.A261V2
chr4:100129989-100129989p.G222*1
chr4:100134823-100134823p.G68C1
chr4:100126162-100126162p.L341F1
chr4:100131323-100131323p.I161M1
chr4:100137350-100137350p.A30T1
chr4:100129878-100129878p.T259S1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 81 1    111   135 7
# mutation31 81 1    121   167 8
nonsynonymous SNV31 8       10    96 8
synonymous SNV    1 1    21   71  
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr4:100137326p.R38C,ADH64
chr4:100129959p.F147L,ADH62
chr4:100131365p.K232E,ADH62
chr4:100131284p.E339D,ADH61
chr4:100137409p.G202A,ADH61
chr4:100126133p.S119P,ADH61
chr4:100131439p.P31Q,ADH61
chr4:100129920p.D335H,ADH61
chr4:100134848p.L201M,ADH61
chr4:100131292p.G110C,ADH61

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for ADH6 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: 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]

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Gene Expression for ADH6

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ADH6,C11orf88,C1orf158,ADGB,C6orf118,C9orf171,CCDC17,
CDHR4,KCNRG,MORN5,SLC51B,ROPN1L,RSPH4A,SNTN,
TEKT1,CATSPERD,TMEM190,TMEM212,TTC29,TUBA4B,CFAP52
ABCG8,ADH1B,ADH6,ANTXR2,HILPDA,CLDN2,ENOX1,
EPHA3,EYS,GPR64,KCNJ8,TENM3___TENM1,PABPC5,PFKFB3,
PLSCR4,RFTN2,RGS17,RNF125,ROBO1,STXBP6,AGMO

ACADS,ACOT11,ADH6,ALDH2,BDH1,C2orf72,CALML4,
CES3,CRYM,DEGS2,EPHX2,GGT6,GPA33,HADH,
LIMA1,LRRC28,NDRG2,PIGR,STARD5,TTC38,TUBAL3
ADH6,AFG3L2,ANO10,ARHGAP18,CMBL,CTAGE5,CTH,
DHRS11,GIPC2,GJB1,HSD17B11,PAFAH2,PROSC,RNF128,
SCP2,SGPL1,SLC19A3,SLC39A5,STRADB,TMBIM6,TMEM19
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for ADH6
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00898alcohol dehydrogenase 6 (class V)approvedEthanol


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Cross referenced IDs for ADH6
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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