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 UCK1
Basic gene info.Gene symbolUCK1
Gene nameuridine-cytidine kinase 1
SynonymsURK1
CytomapUCSC genome browser: 9q34.13
Genomic locationchr9 :134399182-134406662
Type of geneprotein-coding
RefGenesNM_001135954.1,
NM_001261450.1,NM_001261451.1,NM_031432.2,
Ensembl idENSG00000130717
DescriptionUCK 1cytidine monophosphokinase 1uridine monophosphokinase 1
Modification date20141207
dbXrefs MIM : 609328
HGNC : HGNC
Ensembl : ENSG00000130717
HPRD : 18256
Vega : OTTHUMG00000020823
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UCK1
BioGPS: 83549
Gene Expression Atlas: ENSG00000130717
The Human Protein Atlas: ENSG00000130717
PathwayNCI Pathway Interaction Database: UCK1
KEGG: UCK1
REACTOME: UCK1
ConsensusPathDB
Pathway Commons: UCK1
MetabolismMetaCyc: UCK1
HUMANCyc: UCK1
RegulationEnsembl's Regulation: ENSG00000130717
miRBase: chr9 :134,399,182-134,406,662
TargetScan: NM_001135954
cisRED: ENSG00000130717
ContextiHOP: UCK1
cancer metabolism search in PubMed: UCK1
UCL Cancer Institute: UCK1
Assigned class in ccmGDBC

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Phenotypic Information for UCK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UCK1
Familial Cancer Database: UCK1
* 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: UCK1
MedGen: UCK1 (Human Medical Genetics with Condition)
ClinVar: UCK1
PhenotypeMGI: UCK1 (International Mouse Phenotyping Consortium)
PhenomicDB: UCK1

Mutations for UCK1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UCK1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF203809BRSK12273195579589855800890UCK12696899134404397134406032

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

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr9:134400533-134400533p.S243F2
chr9:134404407-134404407p.R176L2
chr9:134406559-134406559p.M1I2
chr9:134401335-134401335p.P211P2
chr9:134401365-134401365p.?1
chr9:134404559-134404559p.R155H1
chr9:134400497-134400497p.P255L1
chr9:134405877-134405877p.H88Q1
chr9:134404332-134404332p.P201L1
chr9:134404580-134404580p.I148T1

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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
# sample   21 2 11      44 9
# mutation   21 2 11      45 9
nonsynonymous SNV    1 2 1       23 7
synonymous SNV   2     1      22 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
chr9:134404542p.D161N,UCK12
chr9:134404543p.R231Q,UCK11
chr9:134405904p.N103N,UCK11
chr9:134400542p.Q219R,UCK11
chr9:134404580p.N103S,UCK11
chr9:134405914p.A194T1
chr9:134400578p.D93H,UCK11
chr9:134404648p.L213P,UCK11
chr9:134405956p.D90D,UCK11
chr9:134400586p.F186F,UCK11

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 UCK1 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 UCK1

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

ANAPC2,C9orf114,C9orf142,ARRDC1-AS1,RABL6,NELFB,COQ4,
DPM2,EDF1,MRPL41,NDOR1,PHPT1,POMT1,PPP2R4,
PTGES2,REXO4,SSNA1,SURF2,UCK1,URM1,USP20
BOLA1,TSR3,CCDC106,CHMP2A,CPSF4,CTDSP1,EXOC3,
FIS1,FKBP8,GRHPR,KLHL22,NDUFB7,PIN1,PSMC3,
RPS19BP1,STUB1,THAP3,UBXN6,UCK1,USE1,WDR13

ANAPC2,ASB6,C9orf114,ARRDC1-AS1,C9orf69,C9orf78,NELFB,
DOLK,INPP5E,LOC100272217,MAPKAP1,MED27,POMT1,SSNA1,
TBC1D13,TMEM203,TOR1A,TRAF2,UCK1,URM1,USP20
AIP,ARL3,FAM227B,C6orf1,CAMLG,CUEDC2,MANBAL,
NINJ1,PPM1M,R3HCC1,RGS10,SIRT2,SNRPN,STOML1,
TPD52L2,UBL4A,UCK1,UROD,ZC3H10,ZMAT5,ZNF691
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 UCK1
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
DB02745uridine-cytidine kinase 1experimentalUridine


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Cross referenced IDs for UCK1
* 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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