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 ADH1C
Basic gene info.Gene symbolADH1C
Gene namealcohol dehydrogenase 1C (class I), gamma polypeptide
SynonymsADH3
CytomapUCSC genome browser: 4q23
Genomic locationchr4 :100257648-100273917
Type of geneprotein-coding
RefGenesNM_000669.4,
Ensembl idENSG00000248144
DescriptionADH, gamma subunitalcohol dehydrogenase 1Calcohol dehydrogenase 3 (class I), gamma polypeptidealdehyde reductase
Modification date20141207
dbXrefs MIM : 103730
HGNC : HGNC
Ensembl : ENSG00000248144
HPRD : 00066
Vega : OTTHUMG00000161422
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADH1C
BioGPS: 126
Gene Expression Atlas: ENSG00000248144
The Human Protein Atlas: ENSG00000248144
PathwayNCI Pathway Interaction Database: ADH1C
KEGG: ADH1C
REACTOME: ADH1C
ConsensusPathDB
Pathway Commons: ADH1C
MetabolismMetaCyc: ADH1C
HUMANCyc: ADH1C
RegulationEnsembl's Regulation: ENSG00000248144
miRBase: chr4 :100,257,648-100,273,917
TargetScan: NM_000669
cisRED: ENSG00000248144
ContextiHOP: ADH1C
cancer metabolism search in PubMed: ADH1C
UCL Cancer Institute: ADH1C
Assigned class in ccmGDBC

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Phenotypic Information for ADH1C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADH1C
Familial Cancer Database: ADH1C
* 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: ADH1C
MedGen: ADH1C (Human Medical Genetics with Condition)
ClinVar: ADH1C
PhenotypeMGI: ADH1C (International Mouse Phenotyping Consortium)
PhenomicDB: ADH1C

Mutations for ADH1C
* 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 ADH1C 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)                 
LOSS (# sample)        1        
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=0

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no ns-snv.There's no s-snv.
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

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 ADH1C 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 ADH1C

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

ACADL,ADH1C,AKR1B15,ALOX15B,CHRNA2,CLDN8,CTNNA2,
ISX,KLHL31,LOC91948,LST-3TM12,NANOG,OR2W5,PGC,
RLN3,RNASE12,SLCO1B1,SPINK8,SPINT3,SRD5A1,UGT2B28
ADH1C,ADH5,ANTXR2,AQP7,AVPI1,PQLC2L,CYB5A,
EBF1,EIF4EBP2,GABARAPL1,GPD1,GTF2E2,GYPE,LARP6,
NRN1,PEX19,PLA2G16,PPP2R5A,PRDX6,RNASE4,EMC3

ADH1C,AMPD1,B3GALT1,ADTRP,CA1,CA2,CDKN2B-AS1,
DRD5,ENTPD5,TMEM236,NXPE1,GBA3,GPR15,PBLD,
PLCE1,SCNN1B,SLC25A34,TMIGD1,UGT1A10,UGT2B15,WSCD1
ADH1C,ALDH3A1,B4GALNT2,BDH1,APMAP,SAYSD1,EHHADH,
FAM45A,GJB1,KCNV1,MEST,AP5M1,NDUFA10,PCCA,
PCTP,PEX11A,RPP25,SH2D4A,STARD7,SUCLG2,TEKT5
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 ADH1C
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 1C (class I), gamma polypeptideapproved; nutraceuticalNADH
DB00898alcohol dehydrogenase 1C (class I), gamma polypeptideapprovedEthanol
DB01213alcohol dehydrogenase 1C (class I), gamma polypeptideapprovedFomepizole
DB01711alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental2,3,4,5,6-Pentafluorobenzyl Alcohol
DB01907alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalNicotinamide-Adenine-Dinucleotide
DB02131alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalN-1-Methylheptylformamide
DB02249alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental2-Ethoxyethanol
DB02659alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalCholic Acid
DB02721alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental4-Iodopyrazole
DB02757alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalPyrazole
DB02822alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalPara-Bromobenzyl Alcohol
DB02871alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental3-Butylthiolane 1-Oxide
DB03020alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental5-Beta-D-Ribofuranosylnicotinamide Adenine Dinucleotide
DB03061alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental(R)-N-(1-Methyl-Hexyl)-Formamide
DB03226alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalTrifluoroethanol
DB03559alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalCyclohexylformamide
DB04071alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalCpad
DB04113alcohol dehydrogenase 1C (class I), gamma polypeptideexperimentalN-Formylpiperidine
DB04312alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental2,3-Difluorobenzyl Alcohol
DB04448alcohol dehydrogenase 1C (class I), gamma polypeptideexperimental2,4-Difluorobenzyl Alcohol 2,4-Difluoro-1-(Hydroxymethyl)Benzene


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Cross referenced IDs for ADH1C
* 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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