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 UPP1

Basic gene info.	Gene symbol	UPP1
	Gene name	uridine phosphorylase 1
	Synonyms	UDRPASE\|UP\|UPASE\|UPP
	Cytomap	UCSC genome browser: 7p12.3
	Genomic location	chr7 :48128745-48148330
	Type of gene	protein-coding
	RefGenes	NM_181597.1, NM_001287426.1,NM_001287428.1,NM_001287429.1,NM_001287430.1, NM_003364.3,NR_109837.1,
	Ensembl id	ENSG00000183696
	Description	UPase 1urdPase 1
	Modification date	20141207
dbXrefs	MIM : 191730
	HGNC : HGNC
	Ensembl : ENSG00000183696
	HPRD : 08932
	Vega : OTTHUMG00000129253
Protein	UniProt: Q16831 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UPP1
	BioGPS: 7378
	Gene Expression Atlas: ENSG00000183696
	The Human Protein Atlas: ENSG00000183696
Pathway	NCI Pathway Interaction Database: UPP1
	KEGG: UPP1
	REACTOME: UPP1
	ConsensusPathDB
	Pathway Commons: UPP1
Metabolism	MetaCyc: UPP1
	HUMANCyc: UPP1
Regulation	Ensembl's Regulation: ENSG00000183696
	miRBase: chr7 :48,128,745-48,148,330
	TargetScan: NM_181597
	cisRED: ENSG00000183696
Context	iHOP: UPP1
	cancer metabolism search in PubMed: UPP1
	UCL Cancer Institute: UPP1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for UPP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: UPP1
	Familial Cancer Database: UPP1

* 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_PYRIMIDINE_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PYRIMIDINE_METABOLISM

Others
OMIM	191730; gene.
Orphanet
Disease	KEGG Disease: UPP1
	MedGen: UPP1 (Human Medical Genetics with Condition)
	ClinVar: UPP1
Phenotype	MGI: UPP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: UPP1

Mutations for UPP1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UPP1 related fusion information.

ID	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
BF808072	UPP1	1	239	7	48146496	48147012	ESYT1	227	501	12	56537665	56537938
BG005429	UPP1	76	182	7	48141424	48141530	UPP1	180	245	7	48134359	48134424
BG012356	UPP1	38	99	7	48134359	48134420	UPP1	97	347	7	48134402	48141530

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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr7:48147911-48147911	p.R297Q	2
chr7:48147020-48147020	p.E237K	2
chr7:48147844-48147844	p.R275C	2
chr7:48141477-48141477	p.G73G	1
chr7:48147874-48147874	p.R285C	1
chr7:48146546-48146546	p.V171V	1
chr7:48139293-48139293	p.P24L	1
chr7:48146991-48146991	p.Y227S	1
chr7:48141512-48141512	p.Y85S	1
chr7:48147888-48147888	p.S289S	1

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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=1

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		3		5	1		3					7	4	1			2	2		7
# mutation		3		5	2		3					8	4	1			2	2		7
nonsynonymous SNV		3		4	2		1					8	3	1				1		5
synonymous SNV				1			2						1				2	1		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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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
chr7:48142961	p.K28R,UPP1	1
chr7:48146663	p.G36W,UPP1	1
chr7:48139333	p.R138C,UPP1	1
chr7:48147888	p.D32N,UPP1	1
chr7:48143002	p.G36G,UPP1	1
chr7:48146983	p.R148C,UPP1	1
chr7:48139359	p.F37L,UPP1	1
chr7:48147906	p.R38W,UPP1	1
chr7:48146546	p.S152S,UPP1	1
chr7:48146991	p.F46S,UPP1	1

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 UPP1 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 UPP1

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


ADA,ARPC1B,BATF3,BRI3,MILR1,CCM2,COL6A2, CYBA,EFNB1,EMP3,HOMER3,LCE3D,LCE3E,LGALS1, PGF,PLTP,PRKCDBP,RARRES2,RCN3,S100A3,UPP1	A4GALT,ARPC1B,C1QA,TOR4A,EFHD2,FCGRT,FES, GMFG,HPCAL1,LYL1,METRNL,MFRP,MGAT1,PLOD3, RENBP,RHOG,RNH1,TGFB1,TNFRSF1A,TNFRSF1B,UPP1

ATG101,SMIM12,CIB1,CLTB,ISG20,KRT19,MYL12B, OASL,PARP12,PHLDA2,PLAUR,POLD4,RAB4B,RHOC, RHOD,RHOF,RHOG,S100A10,S100A16,VIMP,UPP1	AMD1,ARPC4,GSKIP,C20orf24,CSTB,CSTF2,CYB5R4, GTF2A2,LOC541471,MRPS11,NAT1,LINC00152,NDUFB9,NMNAT1, OASL,ORMDL2,PKD2L1,STK17A,TUBA1C,UPP1,UQCRFS1

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 UPP1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q16831; -.
Chemistry	ChEMBL	CHEMBL4811; -.
Organism-specific databases	PharmGKB	PA365; -.
Organism-specific databases	CTD	7378; -.

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
DB07437	uridine phosphorylase 1	experimental	1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE
DB01101	uridine phosphorylase 1	approved; investigational	Capecitabine
DB00544	uridine phosphorylase 1	approved	Fluorouracil
DB00184	uridine phosphorylase 1	approved	Nicotine
DB02745	uridine phosphorylase 1	experimental	Uridine

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Cross referenced IDs for UPP1

* 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