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 UGT1A9
Basic gene info.Gene symbolUGT1A9
Gene nameUDP glucuronosyltransferase 1 family, polypeptide A9
SynonymsHLUGP4|LUGP4|UDPGT|UDPGT 1-9|UGT-1I|UGT1-09|UGT1-9|UGT1.9|UGT1AI|UGT1I
CytomapUCSC genome browser: 2q37
Genomic locationchr2 :234580543-234681951
Type of geneprotein-coding
RefGenesNM_021027.2,
Ensembl idENSG00000241119
DescriptionUDP glycosyltransferase 1 family, polypeptide A9UDP-glucuronosyltransferase 1-9UDP-glucuronosyltransferase 1-IUDP-glucuronosyltransferase 1A9
Modification date20141222
dbXrefs MIM : 606434
HGNC : HGNC
Ensembl : ENSG00000241119
HPRD : 07073
Vega : OTTHUMG00000059124
ProteinUniProt: O60656
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT1A9
BioGPS: 54600
Gene Expression Atlas: ENSG00000241119
The Human Protein Atlas: ENSG00000241119
PathwayNCI Pathway Interaction Database: UGT1A9
KEGG: UGT1A9
REACTOME: UGT1A9
ConsensusPathDB
Pathway Commons: UGT1A9
MetabolismMetaCyc: UGT1A9
HUMANCyc: UGT1A9
RegulationEnsembl's Regulation: ENSG00000241119
miRBase: chr2 :234,580,543-234,681,951
TargetScan: NM_021027
cisRED: ENSG00000241119
ContextiHOP: UGT1A9
cancer metabolism search in PubMed: UGT1A9
UCL Cancer Institute: UGT1A9
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of UGT1A9 in cancer cell metabolism1. Wassenaar CA, Conti DV, Das S, Chen P, Cook EH, et al. (2015) UGT1A and UGT2B genetic variation alters nicotine and nitrosamine glucuronidation in European and African American smokers. Cancer Epidemiology Biomarkers & Prevention 24: 94-104. go to article
2. Laverdiere I, Flageole C, Audet-Walsh É, Caron P, Fradet Y, et al. (2015) The UGT1 locus is a determinant of prostate cancer recurrence after prostatectomy. Endocrine-related cancer 22: 77-85. go to article

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Phenotypic Information for UGT1A9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT1A9
Familial Cancer Database: UGT1A9
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 191740; gene.
606434; gene.
Orphanet
DiseaseKEGG Disease: UGT1A9
MedGen: UGT1A9 (Human Medical Genetics with Condition)
ClinVar: UGT1A9
PhenotypeMGI: UGT1A9 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT1A9

Mutations for UGT1A9
* 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 UGT1A9 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=70)
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
chr2:234581341-234581341p.R254Q5
chr2:234581022-234581022p.D148N5
chr2:234676526-234676526p.S340L3
chr2:234580708-234580708p.S43L3
chr2:234681161-234681161p.K517E3
chr2:234581300-234581300p.T240T2
chr2:234680936-234680936p.S442G2
chr2:234580633-234580633p.L18P2
chr2:234581415-234581415p.Q279E2
chr2:234580975-234580975p.K132T2

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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
# sample1  112   2  733  122 4
# mutation1  102   2  843  143 4
nonsynonymous SNV1  82   1  642  112 3
synonymous SNV   2    1  2 1  31 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
chr2:234581022p.T255T3
chr2:234581345p.D148N3
chr2:234580975p.R254Q2
chr2:234581152p.P191H2
chr2:234581341p.R103Q2
chr2:234581244p.K132I2
chr2:234580888p.R222C2
chr2:234581133p.S43S1
chr2:234580709p.P164L1
chr2:234581300p.T240T1

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 UGT1A9 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 UGT1A9

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

AKR1C1,ALDH3A1,USB1,C20orf196,DNAJB3,G6PD,GPX2,
IQCF2,LOC285629,LSG1,OPA1,RBMXL2,SPTLC3,TBC1D26,
UGT1A1,UGT1A3,UGT1A5,UGT1A6,UGT1A9,VCX,VCX3A
C1orf94,CAPNS2,HMOX1,IL36RN,IL36A,KRT4,KRT6A,
OR2AG1,OR8D1,RPTN,SNORA19,SNORA21,SNORA54,SPRR2A,
SPRR2C,SPRR2E,SPRR3,TMPRSS11A,UGT1A9,UPK1B,VENTXP1

AKR1B10,AKR1C1,AKR1C3,MIEN1,DNAJB3,ERBB2,MED24,
ORMDL3,OSGIN1,PGAP3,PPP1R1B,PSMD3,RGSL1,SNAR-A2,
STARD3,THRA,UGT1A10,UGT1A6,UGT1A7,UGT1A8,UGT1A9
ABCG2,ACVR2A,AKR1B10,AP1AR,BMF,CDC14A,CTAGE5,
FAM73B,FLVCR2,GLS,LPCAT3,MIA2,PDXP,PUS10,
RBKS,RHOU,SLC30A1,SNX24,SLC35G1,UGT1A9,USP2
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 UGT1A9
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O60656; -.
ChemistryChEMBL CHEMBL1743319; -.
Organism-specific databasesPharmGKB PA419; -.
Organism-specific databasesCTD 54600; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB04552UDP glucuronosyltransferase 1 family, polypeptide A9approvedNiflumic Acid
DB04824UDP glucuronosyltransferase 1 family, polypeptide A9withdrawnPhenolphthalein
DB00877UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalSirolimus
DB01024UDP glucuronosyltransferase 1 family, polypeptide A9approvedMycophenolic acid
DB00252UDP glucuronosyltransferase 1 family, polypeptide A9approvedPhenytoin
DB00842UDP glucuronosyltransferase 1 family, polypeptide A9approvedOxazepam
DB00317UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalGefitinib
DB00864UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalTacrolimus
DB00184UDP glucuronosyltransferase 1 family, polypeptide A9approvedNicotine
DB00224UDP glucuronosyltransferase 1 family, polypeptide A9approvedIndinavir
DB00196UDP glucuronosyltransferase 1 family, polypeptide A9approvedFluconazole
DB01026UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalKetoconazole
DB00398UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalSorafenib
DB03496UDP glucuronosyltransferase 1 family, polypeptide A9experimental; investigationalFlavopiridol
DB00818UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalPropofol
DB00688UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalMycophenolate mofetil
DB00762UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalIrinotecan
DB00316UDP glucuronosyltransferase 1 family, polypeptide A9approvedAcetaminophen
DB00355UDP glucuronosyltransferase 1 family, polypeptide A9approvedAztreonam
DB00250UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalDapsone
DB00494UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalEntacapone
DB00598UDP glucuronosyltransferase 1 family, polypeptide A9approvedLabetalol
DB00571UDP glucuronosyltransferase 1 family, polypeptide A9approved; investigationalPropranolol
DB00323UDP glucuronosyltransferase 1 family, polypeptide A9approved; withdrawnTolcapone
DB00695UDP glucuronosyltransferase 1 family, polypeptide A9approvedFurosemide
DB06697UDP glucuronosyltransferase 1 family, polypeptide A9approvedArtemether
DB00712UDP glucuronosyltransferase 1 family, polypeptide A9approvedFlurbiprofen
DB01050UDP glucuronosyltransferase 1 family, polypeptide A9approvedIbuprofen
DB01009UDP glucuronosyltransferase 1 family, polypeptide A9approvedKetoprofen
DB00451UDP glucuronosyltransferase 1 family, polypeptide A9approvedLevothyroxine


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Cross referenced IDs for UGT1A9
* 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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