Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ADH5
Basic gene info.Gene symbolADH5
Gene namealcohol dehydrogenase 5 (class III), chi polypeptide
SynonymsADH-3|ADHX|FALDH|FDH|GSH-FDH|GSNOR
CytomapUCSC genome browser: 4q23
Genomic locationchr4 :99992129-100009931
Type of geneprotein-coding
RefGenesNM_000671.4,
Ensembl idENSG00000197894
DescriptionS-(hydroxymethyl)glutathione dehydrogenasealcohol dehydrogenase (class III), chi polypeptidealcohol dehydrogenase class chi chainalcohol dehydrogenase class-3alcohol dehydrogenase class-IIIformaldehyde dehydrogenaseglutathione-dependent formaldehyde
Modification date20141207
dbXrefs MIM : 103710
HGNC : HGNC
Ensembl : ENSG00000197894
HPRD : 00064
Vega : OTTHUMG00000161230
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADH5
BioGPS: 128
Gene Expression Atlas: ENSG00000197894
The Human Protein Atlas: ENSG00000197894
PathwayNCI Pathway Interaction Database: ADH5
KEGG: ADH5
REACTOME: ADH5
ConsensusPathDB
Pathway Commons: ADH5
MetabolismMetaCyc: ADH5
HUMANCyc: ADH5
RegulationEnsembl's Regulation: ENSG00000197894
miRBase: chr4 :99,992,129-100,009,931
TargetScan: NM_000671
cisRED: ENSG00000197894
ContextiHOP: ADH5
cancer metabolism search in PubMed: ADH5
UCL Cancer Institute: ADH5
Assigned class in ccmGDBC

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Phenotypic Information for ADH5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADH5
Familial Cancer Database: ADH5
* 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: ADH5
MedGen: ADH5 (Human Medical Genetics with Condition)
ClinVar: ADH5
PhenotypeMGI: ADH5 (International Mouse Phenotyping Consortium)
PhenomicDB: ADH5

Mutations for ADH5
* 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 ADH5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN258364PDCL11449125588991125590812ADH514356749999322099993775
BQ338215ITPK115199149354933693549521ADH519338749999753199997876

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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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
chr4:99993587-99993587p.R369Q3
chr4:99993588-99993588p.R369*3
chr4:100003182-100003182p.H67P2
chr4:99997898-99997898p.C174Y2
chr4:99997568-99997568p.E234K2
chr4:99997596-99997596p.I224I2
chr4:100002521-100002521p.K113K2
chr4:99997879-99997879p.Y180Y1
chr4:99996087-99996087p.T313T1
chr4:100003226-100003226p.L52L1

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 7  2 1  221  33 2
# mutation 1 7  2 1  421  33 2
nonsynonymous SNV 1 4  2 1  321  23  
synonymous SNV   3       1    1  2
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
chr4:99993587p.R369Q3
chr4:99997898p.S337S2
chr4:99993813p.P329Q2
chr4:99993838p.C174Y2
chr4:100003182p.S21F1
chr4:99996169p.K373N1
chr4:100006310p.R369R1
chr4:100006318p.R369R1
chr4:99997935p.T313T1
chr4:99993574p.A302V1

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 ADH5 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 ADH5

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

ADH5,ANXA5,BBS7,CHIC2,CISD2,EIF4E,GAR1,
H2AFZ,HELQ,HNRNPD,LSM6,LAMTOR3,METAP1,OSTC,
PAPSS1,PAQR3,PIGY,SMARCAD1,TIGD2,UBE2D3,ZNF330
ADH5,ANTXR2,FAM213A,PQLC2L,EIF4EBP2,EPB41L4B,FAM89A,
FBXO27,GNAI1,GTDC1,GYG2,MAOA,PDE8A,PEX19,
PRDX6,PRKAR2B,RNASE4,RRAGC,SH3KBP1,UBA2,VAMP3

ADH5,ASNA1,C14orf142,CASP6,CISD2,COPS4,EIF4E,
ELMOD2,MED31,METAP1,MRPL54,PPA2,PRDX3,RPS3A,
SCOC,SELT,TIMM8B,TOMM22,UBE2D3,VPS29,WDR61
ADH5,BTF3L4,FAM204A,COMMD2,COMMD3,FUNDC2,GBAS,
GOLGA7,METTL5,NSL1,PFDN5,PIGY,PRDX3,PRKAG1,
RNF41,RPL24,RSL24D1,RWDD2B,SNAPIN,ZCCHC17,ZNF32
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 ADH5
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
DB00157alcohol dehydrogenase 5 (class III), chi polypeptideapproved; nutraceuticalNADH
DB01907alcohol dehydrogenase 5 (class III), chi polypeptideexperimentalNicotinamide-Adenine-Dinucleotide
DB03704alcohol dehydrogenase 5 (class III), chi polypeptideexperimental12-Hydroxydodecanoic Acid
DB04153alcohol dehydrogenase 5 (class III), chi polypeptideexperimentalS-Hydroxymethyl Glutathione
DB01001alcohol dehydrogenase 5 (class III), chi polypeptideapprovedSalbutamol
DB00898alcohol dehydrogenase 5 (class III), chi polypeptideapprovedEthanol


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Cross referenced IDs for ADH5
* 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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