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 UCK2

Basic gene info.	Gene symbol	UCK2
	Gene name	uridine-cytidine kinase 2
	Synonyms	TSA903\|UK\|UMPK
	Cytomap	UCSC genome browser: 1q23
	Genomic location	chr1 :165796731-165880855
	Type of gene	protein-coding
	RefGenes	NM_012474.4,
	Ensembl id	ENSG00000143179
	Description	cytidine monophosphokinase 2testis-specific protein TSA903uridine kinaseuridine monophosphate kinaseuridine monophosphokinase 2
	Modification date	20141207
dbXrefs	MIM : 609329
	HGNC : HGNC
	HPRD : 01882
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UCK2
	BioGPS: 7371
	Gene Expression Atlas: ENSG00000143179
	The Human Protein Atlas: ENSG00000143179
Pathway	NCI Pathway Interaction Database: UCK2
	KEGG: UCK2
	REACTOME: UCK2
	ConsensusPathDB
	Pathway Commons: UCK2
Metabolism	MetaCyc: UCK2
	HUMANCyc: UCK2
Regulation	Ensembl's Regulation: ENSG00000143179
	miRBase: chr1 :165,796,731-165,880,855
	TargetScan: NM_012474
	cisRED: ENSG00000143179
Context	iHOP: UCK2
	cancer metabolism search in PubMed: UCK2
	UCL Cancer Institute: UCK2
Assigned class in ccmGDB	C

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Phenotypic Information for UCK2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: UCK2
	Familial Cancer Database: UCK2

* 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
Orphanet
Disease	KEGG Disease: UCK2
	MedGen: UCK2 (Human Medical Genetics with Condition)
	ClinVar: UCK2
Phenotype	MGI: UCK2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: UCK2

Mutations for UCK2

* 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
breast	UCK2	chr1	165812695	165812695	TARBP1	chr1	234606036	234606036
breast	UCK2	chr1	165815060	165815060	UCK2	chr1	165824772	165824772
ovary	UCK2	chr1	165799651	165799671	UCK2	chr1	165809237	165809257
ovary	UCK2	chr1	165806755	165806775		chr1	186620824	186620844
ovary	UCK2	chr1	165809173	165809193		chr1	186621524	186621544
ovary	UCK2	chr1	165812688	165812708	UCK2	chr1	165840066	165840086
ovary	UCK2	chr1	165813142	165813162	UCK2	chr1	165818641	165818661
ovary	UCK2	chr1	165847585	165847605	PCMTD2	chr20	62894556	62894576

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 UCK2 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
BU929920	UCK2	1	546	1	165866628	165867173	PID1	536	722	2	229890125	229890308
BF366807	UCK2	5	303	1	165820357	165820657	UCK2	299	425	1	165827684	165827810

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr1:165876938-165876938	p.V222L	3
chr1:165860501-165860501	p.E100*	2
chr1:165865554-165865554	p.R162R	2
chr1:165859446-165859446	p.S35S	2
chr1:165872505-165872505	p.F196L	1
chr1:165859581-165859581	p.Q80Q	1
chr1:165865490-165865490	p.F140F	1
chr1:165875164-165875164	p.K202*	1
chr1:165859599-165859599	p.P86P	1
chr1:165865506-165865506	p.R146R	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=2

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	1	5		6			4					10		1			2			3
# mutation	1	5		5			4					10		1			2			3
nonsynonymous SNV		1		2			4					5		1						3
synonymous SNV	1	4		3								5					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
chr1:165860506	p.S35S	2
chr1:165859446	p.I101I	2
chr1:165876971	p.R119L	1
chr1:165865547	p.V222M	1
chr1:165877020	p.P128P	1
chr1:165860550	p.Q223Q	1
chr1:165865554	p.V131M	1
chr1:165860556	p.P233S	1
chr1:165872437	p.V131V	1
chr1:165860559	p.R249H	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 UCK2 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 UCK2

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


ANP32E,AURKB,CCT3,CDCA3,CDCA7,CKS1B,ECE2, FLAD1,HDGF,ILF2,MRPL9,NOP58,PDSS1,PFDN2, PSMB4,SCNM1,SFT2D2,TIMM8A,UCK2,VPS72,ZNF695	C10orf2,CTBP2,DKC1,DTNB,ELL3,ETV6,FZD1, GRHL1,HS3ST4,KCTD14,LRRC8D,MANEAL,PAICS,PHLDA1, PLCH1,PTK7,SLC12A8,TP53,TRIM46,UCK2,WWC1

CACYBP,CCT3,CKS1B,DAP3,DARS2,DUSP12,EXO1, FH,FLAD1,HDGF,ILF2,MRPL9,MTX1,PRCC, PSMD4,SDHC,SNRPE,TIMM17A,UBE2T,UCHL5,UCK2	ARHGEF16,C1orf210,CDC42BPG,CTSD,EDN3,GPRIN2,IL17RE, IVNS1ABP,LSR,P2RY2,PANK1,PRRG2,SLC26A6,SMPDL3A, SPINT2,STXBP2,TSPAN3,UCK2,VILL,VIPR1,ZFYVE27

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 UCK2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB02097	uridine-cytidine kinase 2	experimental	Cytidine
DB02431	uridine-cytidine kinase 2	experimental	Cytidine-5'-Triphosphate
DB03403	uridine-cytidine kinase 2	experimental	Cytidine-5'-Monophosphate
DB03431	uridine-cytidine kinase 2	experimental	Adenosine-5'-Diphosphate
DB04005	uridine-cytidine kinase 2	experimental	Uridine 5'-Triphosphate
DB04272	uridine-cytidine kinase 2	experimental	Citric Acid
DB02745	uridine-cytidine kinase 2	experimental	Uridine
DB00544	uridine-cytidine kinase 2	approved	Fluorouracil
DB00563	uridine-cytidine kinase 2	approved	Methotrexate

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Cross referenced IDs for UCK2

* 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