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 DPYS
Basic gene info.Gene symbolDPYS
Gene namedihydropyrimidinase
SynonymsDHP|DHPase
CytomapUCSC genome browser: 8q22
Genomic locationchr8 :105391651-105479277
Type of geneprotein-coding
RefGenesNM_001385.2,
Ensembl idENSG00000147647
Descriptiondihydropyrimidine amidohydrolasehydantoinase
Modification date20141207
dbXrefs MIM : 613326
HGNC : HGNC
Ensembl : ENSG00000147647
HPRD : 01960
Vega : OTTHUMG00000164891
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DPYS
BioGPS: 1807
Gene Expression Atlas: ENSG00000147647
The Human Protein Atlas: ENSG00000147647
PathwayNCI Pathway Interaction Database: DPYS
KEGG: DPYS
REACTOME: DPYS
ConsensusPathDB
Pathway Commons: DPYS
MetabolismMetaCyc: DPYS
HUMANCyc: DPYS
RegulationEnsembl's Regulation: ENSG00000147647
miRBase: chr8 :105,391,651-105,479,277
TargetScan: NM_001385
cisRED: ENSG00000147647
ContextiHOP: DPYS
cancer metabolism search in PubMed: DPYS
UCL Cancer Institute: DPYS
Assigned class in ccmGDBC

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Phenotypic Information for DPYS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DPYS
Familial Cancer Database: DPYS
* 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_BETA_ALANINE_METABOLISM
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PYRIMIDINE_METABOLISM

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

Mutations for DPYS
* 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 DPYS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample51    1 1 2  1  2
GAIN (# sample)51    1 1 2  1  2
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=84)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=2)
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
chr8:105463544-105463544p.R118Q4
chr8:105478933-105478933p.F72F4
chr8:105459605-105459605p.E184K4
chr8:105436539-105436539p.R391G4
chr8:105463529-105463529p.P123H3
chr8:105459696-105459696p.K153K3
chr8:105393517-105393517p.R490H3
chr8:105405088-105405088p.T456M2
chr8:105405171-105405171p.F428F2
chr8:105440237-105440237p.R355W2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample41 141 5 3  1961  2410 7
# mutation41 151 5 3  2161  258 8
nonsynonymous SNV41 131 5 2  1451  195 6
synonymous SNV   2    1  71   64 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
chr8:105436539p.R391G5
chr8:105405031p.F428F3
chr8:105405171p.R475Q3
chr8:105459696p.K153K3
chr8:105456608p.R118Q2
chr8:105440237p.F101F2
chr8:105459605p.E184K2
chr8:105459626p.F425V2
chr8:105456623p.R355W2
chr8:105463544p.E177K2

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 DPYS 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 DPYS

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

APOA2,APOB,APOC3,ASGR2,C8A,C8G,C9,
CA5A,CREB3L3,DPYS,F2,FABP1,FGF23,GC,
HP,ITIH1,KNG1,MT1H,MT1M,PLG,SLC17A2
CNNM1,DPYS,ENPP6,FHAD1,FMO1,GPR15,GPRC5D,
HPSE2,KCNMB2,LOC254559,LOC96610,MAP3K15,MEI1,NTRK1,
PHC1,PHF12,SLC16A5,SLC26A10,TMEM178A,TXNDC11,ZNF266

BNC1,SERTM1,BPIFB4,CIDEA,CTSL3P,CYLC2,DPYS,
EPGN,FAM180B,BRINP2,FIGLA,HAS1,HEPN1,HP,
LINC01105,LRP2,OR6C3,PKHD1L1,PTPRQ,RFPL4A,TNNT3
BPIFB4,C4A,CCDC144NL,CD300LG,CHRDL2,CNBD1,CST11,
DEFB124,DPYS,DYDC1,GLYCAM1,LIM2,LOC55908,MARCO,
OR3A4P,REG1A,REG1B,RNASE2,SBSN,SCGB1A1,SNORA22
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 DPYS
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
DB00544dihydropyrimidinaseapprovedFluorouracil


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Cross referenced IDs for DPYS
* 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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