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 UGT1A6
Basic gene info.Gene symbolUGT1A6
Gene nameUDP glucuronosyltransferase 1 family, polypeptide A6
SynonymsGNT1|HLUGP|HLUGP1|UDPGT|UDPGT 1-6|UGT1|UGT1A6S|UGT1F
CytomapUCSC genome browser: 2q37
Genomic locationchr2 :234600320-234681945
Type of geneprotein-coding
RefGenesNM_001072.3,
NM_205862.1,
Ensembl idENSG00000167165
DescriptionUDP glycosyltransferase 1 family, polypeptide A6UDP-glucuronosyltransferase 1 family polypeptide A6sUDP-glucuronosyltransferase 1-6UDP-glucuronosyltransferase 1-FUDP-glucuronosyltransferase 1A6UGT-1FUGT1*6UGT1-06UGT1.6phenol-metabolizing UDP-gluc
Modification date20141211
dbXrefs MIM : 606431
HGNC : HGNC
Ensembl : ENSG00000167165
HPRD : 07071
Vega : OTTHUMG00000059122
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT1A6
BioGPS: 54578
Gene Expression Atlas: ENSG00000167165
The Human Protein Atlas: ENSG00000167165
PathwayNCI Pathway Interaction Database: UGT1A6
KEGG: UGT1A6
REACTOME: UGT1A6
ConsensusPathDB
Pathway Commons: UGT1A6
MetabolismMetaCyc: UGT1A6
HUMANCyc: UGT1A6
RegulationEnsembl's Regulation: ENSG00000167165
miRBase: chr2 :234,600,320-234,681,945
TargetScan: NM_001072
cisRED: ENSG00000167165
ContextiHOP: UGT1A6
cancer metabolism search in PubMed: UGT1A6
UCL Cancer Institute: UGT1A6
Assigned class in ccmGDBC

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Phenotypic Information for UGT1A6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT1A6
Familial Cancer Database: UGT1A6
* 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_ASCORBATE_AND_ALDARATE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_RETINOL_METABOLISM
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_OTHER_ENZYMES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: UGT1A6
MedGen: UGT1A6 (Human Medical Genetics with Condition)
ClinVar: UGT1A6
PhenotypeMGI: UGT1A6 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT1A6

Mutations for UGT1A6
* 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 UGT1A6 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    2      
GAIN (# sample)     1    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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=55)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=2)
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
chr2:234681161-234681161p.K519E3
chr2:234676526-234676526p.S342L3
chr2:234602272-234602272p.R208*3
chr2:234681095-234681095p.V497I2
chr2:234677057-234677057p.A425T2
chr2:234681146-234681146p.R514W2
chr2:234602290-234602290p.V214L2
chr2:234601965-234601965p.L105L2
chr2:234676494-234676494p.?2
chr2:234681041-234681041p.D479N2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 21 2 1  61   83 6
# mutation12 21 2 1  61   83 6
nonsynonymous SNV12 11 1 1  61   41 4
synonymous SNV   1  1         42 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
chr2:234602064p.F138L2
chr2:234601779p.A100D1
chr2:234602164p.S227L1
chr2:234602356p.L232L1
chr2:234601804p.I124I1
chr2:234602172p.S234L1
chr2:234602382p.V236I1
chr2:234601870p.D145V1
chr2:234602181p.I244I1
chr2:234602413p.P151S1

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 UGT1A6 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 UGT1A6

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

AKR1B10,AKR1C1,AKR1C3,ALDH3A1,C20orf196,DNAJB3,G6PD,
GAGE2B,GPX2,IQCF2,LOC285629,RBMXL2,SPTLC3,TRIM16L,
UGT1A1,UGT1A3,UGT1A5,UGT1A6,UGT1A9,VCX,VCX3A
ADH7,AKR1B10,ALDH3A1,LINC01559,CYP4F3,GJB4,GJB6,
GPR115,KRT13,KRT4,KRT6A,SERPINB3,SOX2,SPRR1A,
SPRR2A,SPRR3,TMPRSS4,UGT1A10,UGT1A6,UPK1B,XKRX

AATF,MIEN1,ERBB2,FXYD2,GRB7,KCNA10,MED24,
ORMDL3,OSGIN1,PGAP3,PPP1R1B,PSMD3,RGSL1,SNAR-A2,
STARD3,THRA,UGT1A10,UGT1A6,UGT1A7,UGT1A8,UGT1A9
ABHD13,RGCC,C16orf87,C1orf100,C2orf69,CAAP1,COX11,
CREM,CSN1S1,DNTTIP2,DRD5,EIF1B,LHFPL3,LOC100302650,
RAP2C,RPSAP52,RWDD4,SLC25A16,UGT1A6,USP45,WTAP
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 UGT1A6
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
DB00252UDP glucuronosyltransferase 1 family, polypeptide A6approvedPhenytoin
DB00184UDP glucuronosyltransferase 1 family, polypeptide A6approvedNicotine
DB00313UDP glucuronosyltransferase 1 family, polypeptide A6approved; investigationalValproic Acid
DB00316UDP glucuronosyltransferase 1 family, polypeptide A6approvedAcetaminophen
DB00945UDP glucuronosyltransferase 1 family, polypeptide A6approvedAcetylsalicylic acid
DB00762UDP glucuronosyltransferase 1 family, polypeptide A6approved; investigationalIrinotecan
DB00783UDP glucuronosyltransferase 1 family, polypeptide A6approved; investigationalEstradiol
DB00338UDP glucuronosyltransferase 1 family, polypeptide A6approved; investigationalOmeprazole
DB00788UDP glucuronosyltransferase 1 family, polypeptide A6approvedNaproxen


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Cross referenced IDs for UGT1A6
* 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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