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 DCPS
Basic gene info.Gene symbolDCPS
Gene namedecapping enzyme, scavenger
SynonymsDCS1|HINT-5|HINT5|HSL1
CytomapUCSC genome browser: 11q24.2
Genomic locationchr11 :126173646-126215644
Type of geneprotein-coding
RefGenesNM_014026.4,
Ensembl idENSG00000110063
Descriptiondecapping scavenger enzymeheat shock-like protein 1hint-related 7meGMP-directed hydrolasehistidine triad nucleotide-binding protein 5histidine triad protein member 5homolog of C. elegans 7meGMP-directed hydrolase dcs-1m7GpppX diphosphatasemRNA deca
Modification date20141222
dbXrefs MIM : 610534
HGNC : HGNC
Ensembl : ENSG00000110063
HPRD : 16787
Vega : OTTHUMG00000165829
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DCPS
BioGPS: 28960
Gene Expression Atlas: ENSG00000110063
The Human Protein Atlas: ENSG00000110063
PathwayNCI Pathway Interaction Database: DCPS
KEGG: DCPS
REACTOME: DCPS
ConsensusPathDB
Pathway Commons: DCPS
MetabolismMetaCyc: DCPS
HUMANCyc: DCPS
RegulationEnsembl's Regulation: ENSG00000110063
miRBase: chr11 :126,173,646-126,215,644
TargetScan: NM_014026
cisRED: ENSG00000110063
ContextiHOP: DCPS
cancer metabolism search in PubMed: DCPS
UCL Cancer Institute: DCPS
Assigned class in ccmGDBC

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Phenotypic Information for DCPS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DCPS
Familial Cancer Database: DCPS
* 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
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

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

Mutations for DCPS
* 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 DCPS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV705612DCPS121511126208319126208533C721267554098251340982976

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=31)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr11:126208231-126208231p.F191F3
chr11:126213259-126213259p.D232N3
chr11:126201357-126201357p.R145H3
chr11:126215392-126215392p.E300K2
chr11:126201290-126201290p.?2
chr11:126208221-126208221p.R188Q1
chr11:126174172-126174172p.G66E1
chr11:126215349-126215349p.F285F1
chr11:126176613-126176613p.H117R1
chr11:126176481-126176481p.G73V1

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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
# sample2  5    1  521  1118
# mutation2  5    1  621  1118
nonsynonymous SNV2  4       321   116
synonymous SNV   1    1  3    1  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
chr11:126201357p.R145H3
chr11:126208231p.F191F3
chr11:126213223p.A220T3
chr11:126176565p.T136T1
chr11:126215329p.T154T1
chr11:126176613p.R188Q1
chr11:126215338p.K60I1
chr11:126201304p.R224H1
chr11:126215349p.F63V1
chr11:126201331p.R228I1

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 DCPS 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 DCPS

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

ATP5L,CHEK1,DCPS,FAM118B,FOXRED1,H2AFX,HMBS,
HYLS1,PFN1,POLR2F,PPP1R14B,PUS3,REXO2,RPUSD4,
SRPR,ST14,ST3GAL4,TIMM44,TIMM8B,UQCRH,ZPR1
ALKBH2,APRT,CECR5,DCPS,DDX49,DEAF1,DNAJC4,
DTD1,ERCC1,ETHE1,EXOSC5,GRK6,MRTO4,NHP2,
NOP16,NPM3,PRCC,RPL13A,TSC22D4,VARS,ZMYND19

ADAM15,AGR2,BACE2,C14orf80,RBFA,ECI1,DCPS,
DEAF1,F12,FKBP2,HMBS,NAA38,MTX1,PIH1D1,
PSMB6,PSMC3,RAC3,SLC25A22,TIMM22,TMEM134,WRAP53
COPS7B,DCPS,DNAJC10,EXOSC7,FTSJ1,GNA14,HS6ST2,
IARS,IFI16,KCTD14,MSTO1,NAP1L4,NUCB2,POLR3D,
PRMT1,PRPS1,RAD51D,RUVBL1,S100A11,SLC38A5,TUBG1
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 DCPS
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
DB01649decapping enzyme, scavengerexperimental7-Methyl-Gpppa
DB01960decapping enzyme, scavengerexperimental7n-Methyl-8-Hydroguanosine-5'-Diphosphate
DB03593decapping enzyme, scavengerexperimentalN7-Methyl-Guanosine-5'-Monophosphate
DB03958decapping enzyme, scavengerexperimentalMrna Cap Analog N7-Methyl Gpppg
DB07642decapping enzyme, scavengerexperimental5-{[1-(2-fluorobenzyl)piperidin-4-yl]methoxy}quinazoline-2,4-diamine
DB07643decapping enzyme, scavengerexperimental5-{[1-(2,3-dichlorobenzyl)piperidin-4-yl]methoxy}quinazoline-2,4-diamine
DB07644decapping enzyme, scavengerexperimental5-[(1S)-1-(3-chlorophenyl)ethoxy]quinazoline-2,4-diamine


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Cross referenced IDs for DCPS
* 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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