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 UMPS
Basic gene info.Gene symbolUMPS
Gene nameuridine monophosphate synthetase
SynonymsOPRT
CytomapUCSC genome browser: 3q13
Genomic locationchr3 :124449212-124468119
Type of geneprotein-coding
RefGenesNM_000373.3,
NR_033434.1,NR_033437.1,
Ensembl idENSG00000114491
DescriptionOMPdecaseOPRTaseUMP synthaseorotate phosphoribosyltransferaseorotidine 5'-phosphate decarboxylaseuridine 5'-monophosphate synthase
Modification date20141207
dbXrefs MIM : 613891
HGNC : HGNC
HPRD : 02022
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UMPS
BioGPS: 7372
Gene Expression Atlas: ENSG00000114491
The Human Protein Atlas: ENSG00000114491
PathwayNCI Pathway Interaction Database: UMPS
KEGG: UMPS
REACTOME: UMPS
ConsensusPathDB
Pathway Commons: UMPS
MetabolismMetaCyc: UMPS
HUMANCyc: UMPS
RegulationEnsembl's Regulation: ENSG00000114491
miRBase: chr3 :124,449,212-124,468,119
TargetScan: NM_000373
cisRED: ENSG00000114491
ContextiHOP: UMPS
cancer metabolism search in PubMed: UMPS
UCL Cancer Institute: UMPS
Assigned class in ccmGDBC

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

Mutations for UMPS
* 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 UMPS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DW427610UMPS162223124460050124460256UMPS2232783124459205124459260
AW800517UMPS4743124463070124463140EVC67130457842945784357

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 # sample1                
GAIN (# sample)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=36)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr3:124456785-124456785p.F227F3
chr3:124462808-124462808p.G440G2
chr3:124456654-124456654p.E184K2
chr3:124458954-124458954p.E356*2
chr3:124462839-124462839p.R451C2
chr3:124462860-124462860p.D458H1
chr3:124449396-124449396p.F26F1
chr3:124457035-124457035p.E311K1
chr3:124461082-124461082p.H414H1
chr3:124456509-124456509p.T135T1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1314  1 1  611 133 8
# mutation3315  1 1  711 133 10
nonsynonymous SNV1213    1  411 112 6
synonymous SNV21 2  1    3    21 4
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
chr3:124462839p.R451C2
chr3:124456998p.R459H1
chr3:124449468p.L57V1
chr3:124462850p.D271H1
chr3:124456749p.A64A1
chr3:124457035p.K281N1
chr3:124453942p.G65G1
chr3:124462860p.K296N1
chr3:124456779p.E123E1
chr3:124457045p.L298F1

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 UMPS 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 UMPS

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

ACAD9,TIMMDC1,CMSS1,HMCES,CCDC58,EXO1,GMPS,
ISY1,MBD4,MCM2,MRPL3,MRPS22,NAA50,POLQ,
QTRTD1,TRMT10C,RPN1,RUVBL1,SEC22A,TFDP2,UMPS
APH1A,APTX,EIF3D,FBL,ILF2,KRTCAP3,NCOA5,
OCIAD2,PGAP2,POLR1C,PPAP2C,PRSS8,RAB25,RPS4X,
SF3A3,SSRP1,NELFCD,TMEM125,TMEM199,TRIM27,UMPS

ACTL6A,CMSS1,CCDC58,ECE2,FBXO45,GMPS,GNL3,
LSM3,MAD2L1,MCM2,MRPL3,MRPS22,POLR2H,RFC4,
TRMT10C,RUVBL1,SGOL1,SUV39H2,TOMM70A,TRA2B,UMPS
ABCE1,CCT2,CCT5,CCT6A,CCT8,DKC1,EBNA1BP2,
EIF3I,EIF4A1,EIF4A3,FARSB,FASTKD2,HNRNPF,METTL1,
MRPL3,NOL11,PHB,RANBP1,SRPRB,UMPS,UTP6
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 UMPS
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
DB00515uridine monophosphate synthetaseapprovedCisplatin
DB00544uridine monophosphate synthetaseapprovedFluorouracil
DB00526uridine monophosphate synthetaseapproved; investigationalOxaliplatin
DB00130uridine monophosphate synthetaseapproved; nutraceutical; investigationalL-Glutamine
DB00650uridine monophosphate synthetaseapprovedLeucovorin


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Cross referenced IDs for UMPS
* 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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