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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ADH5 |
Basic gene info. | Gene symbol | ADH5 |
Gene name | alcohol dehydrogenase 5 (class III), chi polypeptide | |
Synonyms | ADH-3|ADHX|FALDH|FDH|GSH-FDH|GSNOR | |
Cytomap | UCSC genome browser: 4q23 | |
Genomic location | chr4 :99992129-100009931 | |
Type of gene | protein-coding | |
RefGenes | NM_000671.4, | |
Ensembl id | ENSG00000197894 | |
Description | S-(hydroxymethyl)glutathione dehydrogenasealcohol dehydrogenase (class III), chi polypeptidealcohol dehydrogenase class chi chainalcohol dehydrogenase class-3alcohol dehydrogenase class-IIIformaldehyde dehydrogenaseglutathione-dependent formaldehyde | |
Modification date | 20141207 | |
dbXrefs | MIM : 103710 | |
HGNC : HGNC | ||
Ensembl : ENSG00000197894 | ||
HPRD : 00064 | ||
Vega : OTTHUMG00000161230 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ADH5 | |
BioGPS: 128 | ||
Gene Expression Atlas: ENSG00000197894 | ||
The Human Protein Atlas: ENSG00000197894 | ||
Pathway | NCI Pathway Interaction Database: ADH5 | |
KEGG: ADH5 | ||
REACTOME: ADH5 | ||
ConsensusPathDB | ||
Pathway Commons: ADH5 | ||
Metabolism | MetaCyc: ADH5 | |
HUMANCyc: ADH5 | ||
Regulation | Ensembl's Regulation: ENSG00000197894 | |
miRBase: chr4 :99,992,129-100,009,931 | ||
TargetScan: NM_000671 | ||
cisRED: ENSG00000197894 | ||
Context | iHOP: ADH5 | |
cancer metabolism search in PubMed: ADH5 | ||
UCL Cancer Institute: ADH5 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for ADH5(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: ADH5 |
Familial Cancer Database: ADH5 |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic 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 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: ADH5 |
MedGen: ADH5 (Human Medical Genetics with Condition) | |
ClinVar: ADH5 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ADH5 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
CN258364 | PDCL | 1 | 144 | 9 | 125588991 | 125590812 | ADH5 | 143 | 567 | 4 | 99993220 | 99993775 | |
BQ338215 | ITPK1 | 15 | 199 | 14 | 93549336 | 93549521 | ADH5 | 193 | 387 | 4 | 99997531 | 99997876 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=22) | (# total SNVs=9) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr4:99993587-99993587 | p.R369Q | 3 |
chr4:99993588-99993588 | p.R369* | 3 |
chr4:100003182-100003182 | p.H67P | 2 |
chr4:99997898-99997898 | p.C174Y | 2 |
chr4:99997568-99997568 | p.E234K | 2 |
chr4:99997596-99997596 | p.I224I | 2 |
chr4:100002521-100002521 | p.K113K | 2 |
chr4:100003129-100003129 | p.A85T | 1 |
chr4:99993813-99993813 | p.S337S | 1 |
chr4:99997879-99997879 | p.Y180Y | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 |   | 7 |   |   | 2 |   | 1 |   |   | 2 | 2 | 1 |   |   | 3 | 3 |   | 2 |
# mutation |   | 1 |   | 7 |   |   | 2 |   | 1 |   |   | 4 | 2 | 1 |   |   | 3 | 3 |   | 2 |
nonsynonymous SNV |   | 1 |   | 4 |   |   | 2 |   | 1 |   |   | 3 | 2 | 1 |   |   | 2 | 3 |   |   |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr4:99993587 | p.R369Q | 3 |
chr4:99997898 | p.S337S | 2 |
chr4:99993813 | p.P329Q | 2 |
chr4:99993838 | p.C174Y | 2 |
chr4:100003129 | p.H67R | 1 |
chr4:99996121 | p.S147F | 1 |
chr4:100003182 | p.E24K | 1 |
chr4:99996169 | p.S144S | 1 |
chr4:100006310 | p.S21F | 1 |
chr4:100006318 | p.K373N | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for ADH5 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | alcohol dehydrogenase 5 (class III), chi polypeptide | approved; nutraceutical | NADH | ||
DB01907 | alcohol dehydrogenase 5 (class III), chi polypeptide | experimental | Nicotinamide-Adenine-Dinucleotide | ||
DB03704 | alcohol dehydrogenase 5 (class III), chi polypeptide | experimental | 12-Hydroxydodecanoic Acid | ||
DB04153 | alcohol dehydrogenase 5 (class III), chi polypeptide | experimental | S-Hydroxymethyl Glutathione | ||
DB01001 | alcohol dehydrogenase 5 (class III), chi polypeptide | approved | Salbutamol | ||
DB00898 | alcohol dehydrogenase 5 (class III), chi polypeptide | approved | Ethanol |
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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 |
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