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 DCP1A
Basic gene info.Gene symbolDCP1A
Gene namedecapping mRNA 1A
SynonymsHSA275986|Nbla00360|SMAD4IP1|SMIF
CytomapUCSC genome browser: 3p21.1
Genomic locationchr3 :53317444-53381654
Type of geneprotein-coding
RefGenesNM_001290204.1,
NM_001290205.1,NM_001290206.1,NM_001290207.1,NM_018403.6,
Ensembl idENSG00000162290
DescriptionDCP1 decapping enzyme homolog ASmad4-interacting transcriptional co-activatordecapping enzyme hDcp1amRNA-decapping enzyme 1Aputative protein product of Nbla00360transcription factor SMIF
Modification date20141207
dbXrefs MIM : 607010
HGNC : HGNC
Ensembl : ENSG00000272886
HPRD : 06113
Vega : OTTHUMG00000158193
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DCP1A
BioGPS: 55802
Gene Expression Atlas: ENSG00000162290
The Human Protein Atlas: ENSG00000162290
PathwayNCI Pathway Interaction Database: DCP1A
KEGG: DCP1A
REACTOME: DCP1A
ConsensusPathDB
Pathway Commons: DCP1A
MetabolismMetaCyc: DCP1A
HUMANCyc: DCP1A
RegulationEnsembl's Regulation: ENSG00000162290
miRBase: chr3 :53,317,444-53,381,654
TargetScan: NM_001290204
cisRED: ENSG00000162290
ContextiHOP: DCP1A
cancer metabolism search in PubMed: DCP1A
UCL Cancer Institute: DCP1A
Assigned class in ccmGDBC

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Phenotypic Information for DCP1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DCP1A
Familial Cancer Database: DCP1A
* 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: DCP1A
MedGen: DCP1A (Human Medical Genetics with Condition)
ClinVar: DCP1A
PhenotypeMGI: DCP1A (International Mouse Phenotyping Consortium)
PhenomicDB: DCP1A

Mutations for DCP1A
* 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 DCP1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ277160DCP1A246835332646453381554DCP1A46476835335343453381473
AA368822DCP1A18235332432753324408CSH282107176194993761949962

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=21)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr3:53376254-53376254p.N74S2
chr3:53353455-53353455p.R117H2
chr3:53326317-53326317p.L389F1
chr3:53381533-53381533p.L4L1
chr3:53326747-53326747p.L245L1
chr3:53321675-53321675p.D558N1
chr3:53353456-53353456p.R117C1
chr3:53326366-53326366p.Q372H1
chr3:53338202-53338202p.?1
chr3:53322146-53322146p.Q535Q1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2424  2    41   3315
# mutation2424  2    51   3315
nonsynonymous SNV1222  2    41   11 3
synonymous SNV12 2       1    2212
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
chr3:53326488p.Q305L,DCP1A1
chr3:53346310p.L86L,DCP1A1
chr3:53324879p.P264L,DCP1A1
chr3:53326499p.P52L,DCP1A1
chr3:53346358p.G254W,DCP1A1
chr3:53326214p.P81S,DCP1A1
chr3:53326592p.T250T,DCP1A1
chr3:53346369p.E46K,DCP1A1
chr3:53326245p.S232S,DCP1A1
chr3:53326674p.D45Y,DCP1A1

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 DCP1A 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 DCP1A

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

ACTR8,APPL1,FAM208A,CREBRF,DCP1A,DENND6A,KIAA1109,
KIAA1143,NEK4,PBRM1,PPP4R2,PRKAR2A,RAD54L2,SACM1L,
SETD2,SLMAP,TMF1,TTBK2,VPRBP,WDR82,ZNF445
ANKRD12,ARID4A,ATRX,C16orf52,FAM208A,CAPN7,CEP120,
CTDSPL2,DCP1A,DENND4C,DIS3,FAM135A,HACE1,MON2,
MORC3,RUFY2,SCAF11,USP8,ZDHHC17,ZNF280D,ZNF451

ACTR8,ASXL2,CAPN7,CLASP2,DCP1A,EAF1,KIF2A,
LATS1,NEK4,PBRM1,PPP4R2,PRKAR2A,QRICH1,RAD54L2,
RAPGEF6,RIF1,RPP14,SMARCC1,VHL,VPRBP,WDR82
NSRP1,DCP1A,EIF5B,HNRNPA3,INTS6,ITPRIP,KIF5B,
LUC7L2,MAP4K5,MED1,PBRM1,PNN,RBBP6,RPGR,
NEMF,SEC63,SRRM1,TAF2,TCERG1,TUBGCP3,UPF2
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 DCP1A


There's no related Drug.
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Cross referenced IDs for DCP1A
* 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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