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 UGT1A10
Basic gene info.Gene symbolUGT1A10
Gene nameUDP glucuronosyltransferase 1 family, polypeptide A10
SynonymsUDPGT|UGT-1J|UGT1-10|UGT1.10|UGT1J
CytomapUCSC genome browser: 2q37
Genomic locationchr2 :234545122-234681951
Type of geneprotein-coding
RefGenesNM_019075.2,
Ensembl idENSG00000242515
DescriptionUDP glycosyltransferase 1 family, polypeptide A10UDP-glucuronosyltransferase 1-10UDP-glucuronosyltransferase 1-JUDP-glucuronosyltransferase 1A10UDPGT 1-10
Modification date20141211
dbXrefs MIM : 606435
HGNC : HGNC
Ensembl : ENSG00000242515
HPRD : 07336
Vega : OTTHUMG00000059121
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT1A10
BioGPS: 54575
Gene Expression Atlas: ENSG00000242515
The Human Protein Atlas: ENSG00000242515
PathwayNCI Pathway Interaction Database: UGT1A10
KEGG: UGT1A10
REACTOME: UGT1A10
ConsensusPathDB
Pathway Commons: UGT1A10
MetabolismMetaCyc: UGT1A10
HUMANCyc: UGT1A10
RegulationEnsembl's Regulation: ENSG00000242515
miRBase: chr2 :234,545,122-234,681,951
TargetScan: NM_019075
cisRED: ENSG00000242515
ContextiHOP: UGT1A10
cancer metabolism search in PubMed: UGT1A10
UCL Cancer Institute: UGT1A10
Assigned class in ccmGDBC

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Phenotypic Information for UGT1A10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT1A10
Familial Cancer Database: UGT1A10
* 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: UGT1A10
MedGen: UGT1A10 (Human Medical Genetics with Condition)
ClinVar: UGT1A10
PhenotypeMGI: UGT1A10 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT1A10

Mutations for UGT1A10
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryUGT1A10chr2234550570234550590UGT1A10chr2234546248234546268
pancreasUGT1A10chr2234550459234550479chr93562112135621141
pancreasUGT1A10chr2234580972234580992USP40chr2234444859234444879
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 UGT1A10 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 2      
GAIN (# sample)     1  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=54)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=2)
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
chr2:234545724-234545724p.P186A4
chr2:234681161-234681161p.K517E3
chr2:234545342-234545342p.V58V3
chr2:234545533-234545533p.S122L3
chr2:234676526-234676526p.S340L3
chr2:234545582-234545582p.K138K2
chr2:234681095-234681095p.V495I2
chr2:234677057-234677057p.A423T2
chr2:234681146-234681146p.R512W2
chr2:234545590-234545590p.S141Y2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 12 2 2 11032  131 8
# mutation12 12 2 2 11332  131 9
nonsynonymous SNV 2  1 2 1 1922  91 7
synonymous SNV1  11   1  41   4  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
chr2:234545533p.S122L4
chr2:234545731p.S188F2
chr2:234545590p.S141Y2
chr2:234545613p.P149S2
chr2:234545224p.P9P1
chr2:234545658p.R88R1
chr2:234545342p.K159E1
chr2:234545895p.H278N1
chr2:234545534p.T19I1
chr2:234545236p.M91K1

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 UGT1A10 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 UGT1A10

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

AKR1C3,ALDH3A1,BCL2L10,CCL11,DSCR4,GAGE12J,GAGE2B,
GAGE8,GPR50,GPX2,IQCF2,KRTAP5-4,LOC285629,PRAMEF12,
RBMXL2,UGT1A10,UGT1A5,VCX,VCX3A,VCX3B,VCY
ANXA10,BAAT,GKN2,KRTAP13-1,LGSN,MAGEA4,NAPSA,
NKX2-1,PAEP,BPIFA1,PSAPL1,SCGB3A2,SFTA2,SFTA3,
SFTPB,SFTPC,SLC26A9,SPINK1,TM4SF20,TM4SF5,UGT1A10

ABCC3,AKR1B10,AXDND1,EHHADH,ENTPD5,KRAS,LYRM5,
MOGAT2,PLCE1,PROL1,SGK2,SLC17A8,SLC23A3,SLC25A34,
SULT1B1,TMEM131,UGP2,UGT1A10,UGT1A6,UGT1A8,UGT1A9
ABCD3,ABHD5,ACOX1,AGFG2,ALAS1,CDH17,RHOV___CHP1,
CUL3,EHHADH,HSD17B2,IQGAP2,OPN3,PAPSS2,SFXN1,
SLC22A5,SLC41A2,STK38,TGFA,UGT1A10,UGT1A8,VDAC1
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 UGT1A10
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
DB00184UDP glucuronosyltransferase 1 family, polypeptide A10approvedNicotine
DB00818UDP glucuronosyltransferase 1 family, polypeptide A10approved; investigationalPropofol
DB00762UDP glucuronosyltransferase 1 family, polypeptide A10approved; investigationalIrinotecan
DB00783UDP glucuronosyltransferase 1 family, polypeptide A10approved; investigationalEstradiol


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Cross referenced IDs for UGT1A10
* 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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