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 UGT1A4
Basic gene info.Gene symbolUGT1A4
Gene nameUDP glucuronosyltransferase 1 family, polypeptide A4
SynonymsHUG-BR2|UDPGT|UDPGT 1-4|UGT-1D|UGT1-04|UGT1.4|UGT1D
CytomapUCSC genome browser: 2q37
Genomic locationchr2 :234627437-234681945
Type of geneprotein-coding
RefGenesNM_007120.2,
Ensembl idENSG00000244474
DescriptionUDP glycosyltransferase 1 family, polypeptide A4UDP-glucuronosyltransferase 1-4UDP-glucuronosyltransferase 1-DUDP-glucuronosyltransferase 1A4bilirubin UDP-glucuronosyltransferase isozyme 2bilirubin-specific UDPGT isozyme 2
Modification date20141211
dbXrefs MIM : 606429
HGNC : HGNC
Ensembl : ENSG00000244474
HPRD : 08402
Vega : OTTHUMG00000059119
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT1A4
BioGPS: 54657
Gene Expression Atlas: ENSG00000244474
The Human Protein Atlas: ENSG00000244474
PathwayNCI Pathway Interaction Database: UGT1A4
KEGG: UGT1A4
REACTOME: UGT1A4
ConsensusPathDB
Pathway Commons: UGT1A4
MetabolismMetaCyc: UGT1A4
HUMANCyc: UGT1A4
RegulationEnsembl's Regulation: ENSG00000244474
miRBase: chr2 :234,627,437-234,681,945
TargetScan: NM_007120
cisRED: ENSG00000244474
ContextiHOP: UGT1A4
cancer metabolism search in PubMed: UGT1A4
UCL Cancer Institute: UGT1A4
Assigned class in ccmGDBC

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Phenotypic Information for UGT1A4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT1A4
Familial Cancer Database: UGT1A4
* 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: UGT1A4
MedGen: UGT1A4 (Human Medical Genetics with Condition)
ClinVar: UGT1A4
PhenotypeMGI: UGT1A4 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT1A4

Mutations for UGT1A4
* 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 UGT1A4 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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.K521E3
chr2:234676526-234676526p.S344L3
chr2:234627914-234627914p.L150L3
chr2:234681013-234681013p.G471G2
chr2:234681080-234681080p.G494S2
chr2:234681095-234681095p.V499I2
chr2:234627592-234627592p.L42L2
chr2:234677057-234677057p.A427T2
chr2:234681146-234681146p.R516W2
chr2:234681041-234681041p.D481N2

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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
# sample12261 1 2  412  123 3
# mutation12261 1 2  512  113 3
nonsynonymous SNV1226    2  211  62 3
synonymous SNV    1 1    3 1  51  
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
chr2:234627728p.E88K2
chr2:234627498p.L17P1
chr2:234628211p.V154I1
chr2:234627740p.S253S1
chr2:234627995p.L20L1
chr2:234627516p.A162T1
chr2:234628225p.R258Q1
chr2:234627798p.P24P1
chr2:234628003p.Y164H1
chr2:234627526p.D260D1

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 UGT1A4 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 UGT1A4

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

APCS,APOA2,APOA4,APOC3,C8A,C9,CREB3L3,
CRP,F2,FABP1,FGF23,GDF2,HP,ITIH1,
MT1B,PLG,SERPINA7,SLC17A2,SULT2A1,TM4SF5,UGT1A4
BRS3,CDX2,DKFZp686A1627,DSCR8,GOLGA6L6,KRTAP9-8,LOC348021,
MAGEB2,NR1H4,OR4F4,OR4K15,OR5B17,OR5D16,OR5J2,
POTEB,URAD,PYDC1,SEBOX,SLC22A6,UGT1A4,XAGE2

ABCG2,ALPI,C11orf86,LINC00520,C1orf94,CAPN11,CIDEC,
CLDN23,DHRS9,FAM25BP,GDPD2,GLRA4,LOC646627,MYPN,
NAT8,TRANK1,UGT1A1,UGT1A3,UGT1A4,UGT1A5,VSIG1
ABCC2,ABCG5,ALDOB,APOB,CEACAM20,CYP3A4,DAB1,
DPEP1,FABP6,FGF19,GSTA2,HAPLN4,MGAM,NAT8,
NTS,RBP2,SLC10A2,SLC2A2,SLC34A3,SLC5A12,UGT1A4
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 UGT1A4
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 A4approvedPhenytoin
DB00683UDP glucuronosyltransferase 1 family, polypeptide A4illicit; approvedMidazolam
DB00184UDP glucuronosyltransferase 1 family, polypeptide A4approvedNicotine
DB03255UDP glucuronosyltransferase 1 family, polypeptide A4experimentalPhenol
DB00675UDP glucuronosyltransferase 1 family, polypeptide A4approvedTamoxifen
DB00762UDP glucuronosyltransferase 1 family, polypeptide A4approved; investigationalIrinotecan
DB00477UDP glucuronosyltransferase 1 family, polypeptide A4approvedChlorpromazine
DB00363UDP glucuronosyltransferase 1 family, polypeptide A4approvedClozapine
DB00458UDP glucuronosyltransferase 1 family, polypeptide A4approvedImipramine
DB00555UDP glucuronosyltransferase 1 family, polypeptide A4approved; investigationalLamotrigine
DB00454UDP glucuronosyltransferase 1 family, polypeptide A4approvedMeperidine
DB00334UDP glucuronosyltransferase 1 family, polypeptide A4approved; investigationalOlanzapine


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Cross referenced IDs for UGT1A4
* 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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