Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 XDH

Basic gene info.	Gene symbol	XDH
	Gene name	xanthine dehydrogenase
	Synonyms	XO\|XOR
	Cytomap	UCSC genome browser: 2p23.1
	Genomic location	chr2 :31557187-31637611
	Type of gene	protein-coding
	RefGenes	NM_000379.3,
	Ensembl id	ENSG00000158125
	Description	xanthine dehydrogenase/oxidasexanthine oxidoreductase
	Modification date	20141207
dbXrefs	MIM : 607633
	HGNC : HGNC
	Ensembl : ENSG00000158125
	HPRD : 06363
	Vega : OTTHUMG00000099385
Protein	UniProt: P47989 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_XDH
	BioGPS: 7498
	Gene Expression Atlas: ENSG00000158125
	The Human Protein Atlas: ENSG00000158125
Pathway	NCI Pathway Interaction Database: XDH
	KEGG: XDH
	REACTOME: XDH
	ConsensusPathDB
	Pathway Commons: XDH
Metabolism	MetaCyc: XDH
	HUMANCyc: XDH
Regulation	Ensembl's Regulation: ENSG00000158125
	miRBase: chr2 :31,557,187-31,637,611
	TargetScan: NM_000379
	cisRED: ENSG00000158125
Context	iHOP: XDH
	cancer metabolism search in PubMed: XDH
	UCL Cancer Institute: XDH
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of XDH in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM	278300; phenotype. 607633; gene.
Orphanet	93601; Xanthinuria type I.
Disease	KEGG Disease: XDH
	MedGen: XDH (Human Medical Genetics with Condition)
	ClinVar: XDH
Phenotype	MGI: XDH (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	XDH	chr2	31566571	31566591	PPM1B	chr2	44454837	44454857
pancreas	XDH	chr2	31601014	31601034		chr1	100292577	100292597

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows XDH related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

BE774864

XDH

31558648

31558716

LOC146880

110

62745805

62745854

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr2:31589851-31589851	p.Y736F	4
chr2:31621561-31621561	p.R104K	3
chr2:31569684-31569684	p.R1101K	3
chr2:31573079-31573079	p.R881Q	3
chr2:31564236-31564236	p.D1182N	3
chr2:31562393-31562393	p.R1246C	3
chr2:31570430-31570430	p.T1078T	2
chr2:31588394-31588394	p.R825*	2
chr2:31562412-31562412	p.E1239E	2
chr2:31621549-31621549	p.S108N	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	5	4		22	4		6		3			21	10	2			48	15		16
# mutation	6	4		21	4		6		3			21	10	2			74	18		20
nonsynonymous SNV	4	4		14	3		2		2			13	9	1			52	12		14
synonymous SNV	2			7	1		4		1			8	1	1			22	6		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr2:31573079	p.R881Q	3
chr2:31590879	p.F543F	2
chr2:31598300	p.S289L	2
chr2:31572580	p.T1033A	2
chr2:31564236	p.R896W	2
chr2:31591449	p.P276S	2
chr2:31571184	p.F516F	2
chr2:31598392	p.T820T	2
chr2:31588407	p.I715I	2
chr2:31602786	p.P1013H	2

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P47989; -.
Chemistry	ChEMBL	CHEMBL1929; -.
Chemistry	GuidetoPHARMACOLOGY	2646; -.
Organism-specific databases	PharmGKB	PA37404; -.
Organism-specific databases	CTD	7498; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00437	xanthine dehydrogenase	approved	Allopurinol
DB00583	xanthine dehydrogenase	approved	L-Carnitine
DB01685	xanthine dehydrogenase	experimental	4-[5-Pyridin-4-Yl-1h-[1,2,4]Triazol-3-Yl]-Pyridine-2-Carbonitrile
DB03147	xanthine dehydrogenase	experimental	Flavin-Adenine Dinucleotide
DB03328	xanthine dehydrogenase	experimental	dioxothiomolybdenum(VI) ion
DB03841	xanthine dehydrogenase	experimental	Y-700
DB00997	xanthine dehydrogenase	approved; investigational	Doxorubicin
DB00277	xanthine dehydrogenase	approved	Theophylline
DB00898	xanthine dehydrogenase	approved	Ethanol
DB01412	xanthine dehydrogenase	approved	Theobromine
DB00993	xanthine dehydrogenase	approved	Azathioprine
DB00170	xanthine dehydrogenase	approved; nutraceutical	Menadione
DB00563	xanthine dehydrogenase	approved	Methotrexate
DB00201	xanthine dehydrogenase	approved	Caffeine
DB01033	xanthine dehydrogenase	approved	Mercaptopurine
DB00339	xanthine dehydrogenase	approved	Pyrazinamide

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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