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 UGT2A1
Basic gene info.Gene symbolUGT2A1
Gene nameUDP glucuronosyltransferase 2 family, polypeptide A1, complex locus
SynonymsUDPGT2A1
CytomapUCSC genome browser: 4q13
Genomic locationchr4 :70454134-70518967
Type of geneprotein-coding
RefGenesNM_001252274.2,
NM_001252275.2,NM_001301239.1,NM_006798.4,
Ensembl idENSG00000173610
DescriptionUDP glycosyltransferase 2 family, polypeptide A1UDP-glucuronosyltransferase 2A1uridine diphosphate glycosyltransferase 2 family, member A1
Modification date20141207
dbXrefs MIM : 604716
HGNC : HGNC
Ensembl : ENSG00000173610
HPRD : 05279
Vega : OTTHUMG00000184942
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT2A1
BioGPS: 10941
Gene Expression Atlas: ENSG00000173610
The Human Protein Atlas: ENSG00000173610
PathwayNCI Pathway Interaction Database: UGT2A1
KEGG: UGT2A1
REACTOME: UGT2A1
ConsensusPathDB
Pathway Commons: UGT2A1
MetabolismMetaCyc: UGT2A1
HUMANCyc: UGT2A1
RegulationEnsembl's Regulation: ENSG00000173610
miRBase: chr4 :70,454,134-70,518,967
TargetScan: NM_001252274
cisRED: ENSG00000173610
ContextiHOP: UGT2A1
cancer metabolism search in PubMed: UGT2A1
UCL Cancer Institute: UGT2A1
Assigned class in ccmGDBC

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Phenotypic Information for UGT2A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT2A1
Familial Cancer Database: UGT2A1
* 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: UGT2A1
MedGen: UGT2A1 (Human Medical Genetics with Condition)
ClinVar: UGT2A1
PhenotypeMGI: UGT2A1 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT2A1

Mutations for UGT2A1
* 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
ovaryUGT2A1chr47046736370467563UGT2A1chr47047275070472950
ovaryUGT2A1chr47046744870467468UGT2A1chr47047279370472813
ovaryUGT2A1chr47049345070493470UGT2A1chr47049369570493715
ovaryUGT2A1chr47050923670509256UGT2A1chr47050586370505883
pancreasUGT2A1chr47049191170491931UGT2A1chr47049512670495146
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 UGT2A1 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  1     1  
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=59)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=4)
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
chr4:70455340-70455340p.R445I3
chr4:70455304-70455304p.R457Q3
chr4:70455305-70455305p.R457*3
chr4:70465074-70465074p.E252K3
chr4:70513122-70513122p.E81*3
chr4:70460341-70460341p.V386V2
chr4:70455274-70455274p.R467H2
chr4:70465030-70465030p.R266R2
chr4:70465032-70465032p.R266C2
chr4:70512854-70512854p.S170Y2

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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
# sample1  21 5  1 233  82 4
# mutation1  21 5  1 233  82 5
nonsynonymous SNV1  11 3  1 223  52 4
synonymous SNV   1  2     1   3  1
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
chr4:70513300p.G21G,UGT2A12
chr4:70512848p.R211K,UGT2A11
chr4:70513132p.Q109E,UGT2A11
chr4:70512731p.Q11R,UGT2A11
chr4:70513331p.R211R,UGT2A11
chr4:70512912p.Y108F,UGT2A11
chr4:70513145p.R209I,UGT2A11
chr4:70512732p.T103A,UGT2A11
chr4:70512938p.S205Y,UGT2A11
chr4:70513183p.S102L,UGT2A11

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 UGT2A1 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 UGT2A1

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

BRF2,C9orf72,CAAP1,EIF4EBP1,FGF13,FGFR1,HOXB4,
IFT74,IL19,KLRC2,LOC158696,LOC728024,PLAA,PLAC1,
PPAPDC1B,PROSC,RRAGA,SCGB1D4,SPAG16,TUSC3,UGT2A1
C9orf84,CCL27,CRYAA,DEFB109P1B,IL36A,IRGC,KRT3,
KRT84,LOC285740,LINC00159,OR1F1,OR1L1,OTOP3,PPY,
RPTN,SCARNA27,SNORA22,SNORA71D,TSHB,UGT2A1,ZNRF4

CT45A5,CT45A6,CTAG2,CYP2A7,DPY19L2P1,LOC285501,LOC389705,
MAGEA9B,OR1D4,OR2M2,OR5J2,SAGE1,SLC6A13,SPAG11A,
SPAG11B,ST8SIA5,TAAR5,TCERG1L,TCF23,TNFRSF18,UGT2A1
ADH7,AMTN,C6orf15,CT83,PRR32,DUSP13,FOXE1,
GAGE12J,KRT13,KRT34,KRT4,KRT6A,KRTAP4-7,LCE1F,
LCE4A,SERPINB13,SERPINB4,SSX1,SSX2,TMPRSS11A,UGT2A1
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 UGT2A1


There's no related Drug.
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Cross referenced IDs for UGT2A1
* 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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