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 XDH
Basic gene info.Gene symbolXDH
Gene namexanthine dehydrogenase
SynonymsXO|XOR
CytomapUCSC genome browser: 2p23.1
Genomic locationchr2 :31557187-31637611
Type of geneprotein-coding
RefGenesNM_000379.3,
Ensembl idENSG00000158125
Descriptionxanthine dehydrogenase/oxidasexanthine oxidoreductase
Modification date20141207
dbXrefs MIM : 607633
HGNC : HGNC
Ensembl : ENSG00000158125
HPRD : 06363
Vega : OTTHUMG00000099385
ProteinUniProt: P47989
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XDH
BioGPS: 7498
Gene Expression Atlas: ENSG00000158125
The Human Protein Atlas: ENSG00000158125
PathwayNCI Pathway Interaction Database: XDH
KEGG: XDH
REACTOME: XDH
ConsensusPathDB
Pathway Commons: XDH
MetabolismMetaCyc: XDH
HUMANCyc: XDH
RegulationEnsembl's Regulation: ENSG00000158125
miRBase: chr2 :31,557,187-31,637,611
TargetScan: NM_000379
cisRED: ENSG00000158125
ContextiHOP: XDH
cancer metabolism search in PubMed: XDH
UCL Cancer Institute: XDH
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of XDH in cancer cell metabolism1. Matimba A, Li F, Livshits A, Cartwright CS, Scully S, et al. (2014) Thiopurine pharmacogenomics: association of SNPs with clinical response and functional validation of candidate genes. Pharmacogenomics 15: 433-447. go to article

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Phenotypic Information for XDH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: XDH
Familial Cancer Database: XDH
* 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_PURINE_METABOLISM
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM 278300; phenotype.
607633; gene.
Orphanet 93601; Xanthinuria type I.
DiseaseKEGG Disease: XDH
MedGen: XDH (Human Medical Genetics with Condition)
ClinVar: XDH
PhenotypeMGI: XDH (International Mouse Phenotyping Consortium)
PhenomicDB: XDH

Mutations for XDH
* 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
ovaryXDHchr23156657131566591PPM1Bchr24445483744454857
pancreasXDHchr23160101431601034chr1100292577100292597
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 XDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE774864XDH16623155864831558716LOC14688061110176274580562745854

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   
GAIN (# sample)        1    1   
LOSS (# sample)                 
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=125)
Stat. for Synonymous SNVs
(# total SNVs=47)
Stat. for Deletions
(# total SNVs=3)
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
chr2:31589851-31589851p.Y736F4
chr2:31564236-31564236p.D1182N3
chr2:31562393-31562393p.R1246C3
chr2:31621561-31621561p.R104K3
chr2:31569684-31569684p.R1101K3
chr2:31573079-31573079p.R881Q3
chr2:31620593-31620593p.N146H2
chr2:31570422-31570422p.S1081F2
chr2:31621533-31621533p.C113C2
chr2:31598300-31598300p.F516F2

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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
# sample54 224 6 3  21102  4815 16
# mutation64 214 6 3  21102  7418 20
nonsynonymous SNV44 143 2 2  1391  5212 14
synonymous SNV2  71 4 1  811  226 6
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
chr2:31573079p.R881Q3
chr2:31602786p.A1079T2
chr2:31571778p.D1182N2
chr2:31596796p.F543F2
chr2:31570429p.S289L2
chr2:31606641p.T1033A2
chr2:31562483p.R896W2
chr2:31606681p.P276S2
chr2:31573035p.I715I2
chr2:31598300p.F516F2

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 XDH 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 XDH

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

BTN1A1,CD14,CD180,CSN1S1,DMBT1,EDN3,GNLY,
IGFL4,KIR2DL3,LIPG,MRGPRX3,NOS1,OLAH,PDE11A,
PGA5,PTN,SST,TGFBR2,TMEM233,VNN1,XDH
BTN1A1,CEL,CHRDL2,CNGA2,CSN1S1,CSN1S2AP,CSN2,
CSN3,GC,GPRC6A,LALBA,LPO,OLAH,OR52A5,
OR8S1,SEMG2,SLC9A4,SLCO4C1,STATH,TMEM171,XDH

B3GALT5,BCL10,C1orf177,C4orf19,CASP10,CASP5,CCL28,
CLCA3P,DUOX2,DUOXA2,GPT,HK2,MALL,NOS2,
PTPRH,SLC37A1,TMPRSS2,TNIP3,TRIM40,XDH,ZC3H12A
APOL1,APOL6,C18orf8,CASP10,CASP5,CASP8,CLIC5,
DTX3L,GRIN3A,GZMA,HRASLS2,LAP3,MOV10,NOS2,
NUB1,PARP9,PSME2,TAP2,TYMP,USP38,XDH
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 XDH
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P47989; -.
ChemistryChEMBL CHEMBL1929; -.
ChemistryGuidetoPHARMACOLOGY 2646; -.
Organism-specific databasesPharmGKB PA37404; -.
Organism-specific databasesCTD 7498; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00437xanthine dehydrogenaseapprovedAllopurinol
DB00583xanthine dehydrogenaseapprovedL-Carnitine
DB01685xanthine dehydrogenaseexperimental4-[5-Pyridin-4-Yl-1h-[1,2,4]Triazol-3-Yl]-Pyridine-2-Carbonitrile
DB03147xanthine dehydrogenaseexperimentalFlavin-Adenine Dinucleotide
DB03328xanthine dehydrogenaseexperimentaldioxothiomolybdenum(VI) ion
DB03841xanthine dehydrogenaseexperimentalY-700
DB00997xanthine dehydrogenaseapproved; investigationalDoxorubicin
DB00277xanthine dehydrogenaseapprovedTheophylline
DB00898xanthine dehydrogenaseapprovedEthanol
DB01412xanthine dehydrogenaseapprovedTheobromine
DB00993xanthine dehydrogenaseapprovedAzathioprine
DB00170xanthine dehydrogenaseapproved; nutraceuticalMenadione
DB00563xanthine dehydrogenaseapprovedMethotrexate
DB00201xanthine dehydrogenaseapprovedCaffeine
DB01033xanthine dehydrogenaseapprovedMercaptopurine
DB00339xanthine dehydrogenaseapprovedPyrazinamide


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Cross referenced IDs for XDH
* 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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