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 UCK2
Basic gene info.Gene symbolUCK2
Gene nameuridine-cytidine kinase 2
SynonymsTSA903|UK|UMPK
CytomapUCSC genome browser: 1q23
Genomic locationchr1 :165796731-165880855
Type of geneprotein-coding
RefGenesNM_012474.4,
Ensembl idENSG00000143179
Descriptioncytidine monophosphokinase 2testis-specific protein TSA903uridine kinaseuridine monophosphate kinaseuridine monophosphokinase 2
Modification date20141207
dbXrefs MIM : 609329
HGNC : HGNC
HPRD : 01882
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UCK2
BioGPS: 7371
Gene Expression Atlas: ENSG00000143179
The Human Protein Atlas: ENSG00000143179
PathwayNCI Pathway Interaction Database: UCK2
KEGG: UCK2
REACTOME: UCK2
ConsensusPathDB
Pathway Commons: UCK2
MetabolismMetaCyc: UCK2
HUMANCyc: UCK2
RegulationEnsembl's Regulation: ENSG00000143179
miRBase: chr1 :165,796,731-165,880,855
TargetScan: NM_012474
cisRED: ENSG00000143179
ContextiHOP: UCK2
cancer metabolism search in PubMed: UCK2
UCL Cancer Institute: UCK2
Assigned class in ccmGDBC

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Phenotypic Information for UCK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_PYRIMIDINE_METABOLISM
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: UCK2
MedGen: UCK2 (Human Medical Genetics with Condition)
ClinVar: UCK2
PhenotypeMGI: UCK2 (International Mouse Phenotyping Consortium)
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.

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
breastUCK2chr1165812695165812695TARBP1chr1234606036234606036
breastUCK2chr1165815060165815060UCK2chr1165824772165824772
ovaryUCK2chr1165799651165799671UCK2chr1165809237165809257
ovaryUCK2chr1165806755165806775chr1186620824186620844
ovaryUCK2chr1165809173165809193chr1186621524186621544
ovaryUCK2chr1165812688165812708UCK2chr1165840066165840086
ovaryUCK2chr1165813142165813162UCK2chr1165818641165818661
ovaryUCK2chr1165847585165847605PCMTD2chr206289455662894576
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 UCK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU929920UCK215461165866628165867173PID15367222229890125229890308
BF366807UCK253031165820357165820657UCK22994251165827684165827810

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 # sample7  1    1        
GAIN (# sample)7  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=3

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check002.gifSomatic 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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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
chr1:165876938-165876938p.V222L3
chr1:165860501-165860501p.E100*2
chr1:165865554-165865554p.R162R2
chr1:165859446-165859446p.S35S2
chr1:165865450-165865450p.Y127C1
chr1:165872479-165872479p.T187K1
chr1:165876981-165876982p.R236L1
chr1:165859506-165859506p.Q55H1
chr1:165865454-165865454p.P128P1
chr1:165872480-165872480p.T187T1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample15 6  4    10 1  2  3
# mutation15 5  4    10 1  2  3
nonsynonymous SNV 1 2  4    5 1     3
synonymous SNV14 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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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
chr1:165860506p.S35S2
chr1:165859446p.I101I2
chr1:165865490p.R146R1
chr1:165872505p.L148P1
chr1:165859550p.V36A1
chr1:165865506p.F149F1
chr1:165876938p.Q53E1
chr1:165859581p.A159A1
chr1:165865513p.R66R1
chr1:165876943p.R162R1

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 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

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

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
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 UCK2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02097uridine-cytidine kinase 2experimentalCytidine
DB02431uridine-cytidine kinase 2experimentalCytidine-5'-Triphosphate
DB03403uridine-cytidine kinase 2experimentalCytidine-5'-Monophosphate
DB03431uridine-cytidine kinase 2experimentalAdenosine-5'-Diphosphate
DB04005uridine-cytidine kinase 2experimentalUridine 5'-Triphosphate
DB04272uridine-cytidine kinase 2experimentalCitric Acid
DB02745uridine-cytidine kinase 2experimentalUridine
DB00544uridine-cytidine kinase 2approvedFluorouracil
DB00563uridine-cytidine kinase 2approvedMethotrexate


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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



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