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 UGT2B4
Basic gene info.Gene symbolUGT2B4
Gene nameUDP glucuronosyltransferase 2 family, polypeptide B4
SynonymsHLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11
CytomapUCSC genome browser: 4q13
Genomic locationchr4 :70345882-70361626
Type of geneprotein-coding
RefGenesNM_001297615.1,
NM_001297616.1,NM_021139.2,
Ensembl idENSG00000156096
DescriptionUDP-glucuronosyltransferase 2B4UDP-glucuronyltransferase, family 2, beta-4UDPGT 2B4hyodeoxycholic acidhyodeoxycholic acid-specific UDPGT
Modification date20141207
dbXrefs MIM : 600067
HGNC : HGNC
Ensembl : ENSG00000156096
HPRD : 02507
Vega : OTTHUMG00000058891
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT2B4
BioGPS: 7363
Gene Expression Atlas: ENSG00000156096
The Human Protein Atlas: ENSG00000156096
PathwayNCI Pathway Interaction Database: UGT2B4
KEGG: UGT2B4
REACTOME: UGT2B4
ConsensusPathDB
Pathway Commons: UGT2B4
MetabolismMetaCyc: UGT2B4
HUMANCyc: UGT2B4
RegulationEnsembl's Regulation: ENSG00000156096
miRBase: chr4 :70,345,882-70,361,626
TargetScan: NM_001297615
cisRED: ENSG00000156096
ContextiHOP: UGT2B4
cancer metabolism search in PubMed: UGT2B4
UCL Cancer Institute: UGT2B4
Assigned class in ccmGDBC

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Phenotypic Information for UGT2B4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT2B4
Familial Cancer Database: UGT2B4
* 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: UGT2B4
MedGen: UGT2B4 (Human Medical Genetics with Condition)
ClinVar: UGT2B4
PhenotypeMGI: UGT2B4 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT2B4

Mutations for UGT2B4
* 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 UGT2B4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI114505EIF2AK3116928892234988922517UGT2B416063647034588370346360

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
There's no copy number variation information in COSMIC data for this gene.

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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=82)
Stat. for Synonymous SNVs
(# total SNVs=35)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr4:70361046-70361046p.Y178Y3
chr4:70355168-70355168p.I331V3
chr4:70359494-70359494p.D263N3
chr4:70359506-70359506p.R259*3
chr4:70346533-70346533p.R469H3
chr4:70360875-70360875p.F235F2
chr4:70350935-70350935p.N434S2
chr4:70351106-70351106p.A377D2
chr4:70361447-70361447p.E45K2
chr4:70361510-70361510p.G24*2

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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
# sample31186 11 2  2293  342 9
# mutation31286 11 2  25123  393 11
nonsynonymous SNV2 174 8    1692  282 9
synonymous SNV11112 3 2  931  111 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
chr4:70346533p.R469H,UGT2B43
chr4:70361447p.G310W,UGT2B42
chr4:70361517p.L27L,UGT2B42
chr4:70350946p.K430K,UGT2B42
chr4:70346553p.D482N,UGT2B42
chr4:70361563p.D263N,UGT2B42
chr4:70359494p.G21G,UGT2B42
chr4:70355231p.F462L,UGT2B42
chr4:70361499p.G522V,UGT2B42
chr4:70346495p.T6I,UGT2B42

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 UGT2B4 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 UGT2B4

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

ARHGEF18,ATRNL1,C12orf60,CCDC85A,ERLIN2,FLJ34503,GABRA1,
GABRG2,GDAP1,GPATCH2,KCNK4,MRGPRX2,LINC00176,PCDH19,
PEX11G,PRR25,PTPRQ,RD3,UGT2B4,VSIG1,ZNF703
AGXT,ALDOC,BOK,SPX,CDH20,CDKN2C,DGAT2,
ELMOD3,FAM171A2,FGFRL1,GPAM,GPC6,KLB,KRT79,
OPRK1,PRRT4,RASGRF2,SPATA9,SSC4D,THRSP,UGT2B4

ALOX15B,ANXA13,CIB4,CRISP2,GPR37L1,GSTTP1,GSTTP2,
HRASLS5,HSPA2,ICK,ITLN2,KIF19,KLK12,LYZL6,
MAK,GRIK1-AS1,OPRD1,RHBDL3,SHISA3,UGT2B4,UMOD
AFM,ALB,APCS,C3P1,C8A,CFHR2,CFHR5,
CYP4A22,DNAJB8,F13B,F9,KIR3DP1,KRTAP4-11,KRTAP5-3,
LECT2,LOC100129935,LINC00160,OR1N1,SERPINC1,SLC17A2,UGT2B4
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 UGT2B4
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
DB00318UDP glucuronosyltransferase 2 family, polypeptide B4illicit; approvedCodeine
DB00712UDP glucuronosyltransferase 2 family, polypeptide B4approvedFlurbiprofen
DB01050UDP glucuronosyltransferase 2 family, polypeptide B4approvedIbuprofen
DB01009UDP glucuronosyltransferase 2 family, polypeptide B4approvedKetoprofen


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Cross referenced IDs for UGT2B4
* 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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