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 ADHFE1
Basic gene info.Gene symbolADHFE1
Gene namealcohol dehydrogenase, iron containing, 1
SynonymsADH8|HOT
CytomapUCSC genome browser: 8q13.1
Genomic locationchr8 :67344717-67381044
Type of geneprotein-coding
RefGenesNM_144650.2,
Ensembl idENSG00000147576
DescriptionFe-containing alcohol dehydrogenase 1alcohol dehydrogenase 8alcohol dehydrogenase iron-containing protein 1hydroxyacid-oxoacid transhydrogenase, mitochondrial
Modification date20141222
dbXrefs MIM : 611083
HGNC : HGNC
Ensembl : ENSG00000147576
HPRD : 12428
Vega : OTTHUMG00000150215
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADHFE1
BioGPS: 137872
Gene Expression Atlas: ENSG00000147576
The Human Protein Atlas: ENSG00000147576
PathwayNCI Pathway Interaction Database: ADHFE1
KEGG: ADHFE1
REACTOME: ADHFE1
ConsensusPathDB
Pathway Commons: ADHFE1
MetabolismMetaCyc: ADHFE1
HUMANCyc: ADHFE1
RegulationEnsembl's Regulation: ENSG00000147576
miRBase: chr8 :67,344,717-67,381,044
TargetScan: NM_144650
cisRED: ENSG00000147576
ContextiHOP: ADHFE1
cancer metabolism search in PubMed: ADHFE1
UCL Cancer Institute: ADHFE1
Assigned class in ccmGDBC

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Phenotypic Information for ADHFE1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADHFE1
Familial Cancer Database: ADHFE1
* 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
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ADHFE1
MedGen: ADHFE1 (Human Medical Genetics with Condition)
ClinVar: ADHFE1
PhenotypeMGI: ADHFE1 (International Mouse Phenotyping Consortium)
PhenomicDB: ADHFE1

Mutations for ADHFE1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryADHFE1chr86735884167358861ADHFE1chr86736061767360637
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ADHFE1 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 # sample1     1          
GAIN (# sample)1                
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr8:67372616-67372616p.F364F3
chr8:67356917-67356917p.S48F2
chr8:67361196-67361196p.D194G2
chr8:67361109-67361109p.S165L2
chr8:67356836-67356836p.K21R2
chr8:67364250-67364250p.P218L2
chr8:67366351-67366351p.A267A2
chr8:67361171-67361171p.R186*2
chr8:67364258-67364258p.R221W2
chr8:67361172-67361172p.R186Q1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 13  211  421  47 4
# mutation21 12  211  821  48 6
nonsynonymous SNV21 8  211  421  46 4
synonymous SNV   4       4     2 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
chr8:67372616p.F412F3
chr8:67361186p.R392H2
chr8:67372555p.S239R2
chr8:67366351p.A315A2
chr8:67361172p.R379Q1
chr8:67356836p.T115M1
chr8:67369066p.R234R1
chr8:67357525p.D390N1
chr8:67372691p.T115T1
chr8:67361179p.R234Q1

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 ADHFE1 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 ADHFE1

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

ADHFE1,C14orf181,CCDC84,CCNL2,CHKB-CPT1B,CLK1,CLK4,
ECHDC2,JMJD7-PLA2G4B,KLHDC1,MYO15B,PILRB,RBM5,RNF207,
SEC31B,SRSF5,SGSM2,TTLL3,WDR27,ZNF577,ZNF767P
ACAT1,ADHFE1,ATPAF1,CS,DLD,DLST,ETFA,
ETFDH,GPT2,HSDL2,KIAA0408,PDHA1,PDK2,PFKFB1,
PHYH,PLIN5,PPARA,RNF157,SLC2A4,STRADB,SUCLA2

ADAM33,ADHFE1,ANK2,AOC3,ASB2,ATP1A2,CBX7,
CCDC69,FHL1,FNBP1,GNAO1,GPRASP1,LOC728264,MAPK10,
MYOM1,NAP1L2,NEGR1,PDE2A,RIC3,SDPR,SLC9A9
ADAMTS10,ADHFE1,C10orf25,C11orf63,C1orf56,CAPRIN2,DFNB59,
GTF2IRD2P1,LOC100271722,LOC388387,LRRC2,PTH1R,SATB1,SGSM2,
SIX5,TJAP1,TMEM136,TRIM45,VEGFB,ZNF337,ZNF444
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 ADHFE1


There's no related Drug.
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Cross referenced IDs for ADHFE1
* 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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