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 DCP2
Basic gene info.Gene symbolDCP2
Gene namedecapping mRNA 2
SynonymsNUDT20
CytomapUCSC genome browser: 5q22.2
Genomic locationchr5 :112312406-112357892
Type of geneprotein-coding
RefGenesNM_001242377.1,
NM_152624.5,NR_038352.1,
Ensembl idENSG00000172795
DescriptionDCP2 decapping enzyme homologhDpcm7GpppN-mRNA hydrolasemRNA-decapping enzyme 2nudix (nucleoside diphosphate linked moiety X)-type motif 20
Modification date20141207
dbXrefs MIM : 609844
HGNC : HGNC
Ensembl : ENSG00000172795
HPRD : 13125
Vega : OTTHUMG00000162853
ProteinUniProt: Q8IU60
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DCP2
BioGPS: 167227
Gene Expression Atlas: ENSG00000172795
The Human Protein Atlas: ENSG00000172795
PathwayNCI Pathway Interaction Database: DCP2
KEGG: DCP2
REACTOME: DCP2
ConsensusPathDB
Pathway Commons: DCP2
MetabolismMetaCyc: DCP2
HUMANCyc: DCP2
RegulationEnsembl's Regulation: ENSG00000172795
miRBase: chr5 :112,312,406-112,357,892
TargetScan: NM_001242377
cisRED: ENSG00000172795
ContextiHOP: DCP2
cancer metabolism search in PubMed: DCP2
UCL Cancer Institute: DCP2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DCP2 in cancer cell metabolism1. Grudzien-Nogalska E, Jemielity J, Kowalska J, Darzynkiewicz E, Rhoads RE (2007) Phosphorothioate cap analogs stabilize mRNA and increase translational efficiency in mammalian cells. RNA 13: 1745-1755. doi: 10.1261/rna.701307. pmid: 1986804. go to article
2. Mencia N, Selga E, Noe V, Ciudad CJ (2011) Underexpression of miR-224 in methotrexate resistant human colon cancer cells. Biochem Pharmacol 82: 1572-1582. doi: 10.1016/j.bcp.2011.08.009. go to article

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Phenotypic Information for DCP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DCP2
Familial Cancer Database: DCP2
* 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 609844; gene.
Orphanet
DiseaseKEGG Disease: DCP2
MedGen: DCP2 (Human Medical Genetics with Condition)
ClinVar: DCP2
PhenotypeMGI: DCP2 (International Mouse Phenotyping Consortium)
PhenomicDB: DCP2

Mutations for DCP2
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryDCP2chr5112337257112337277chr5112002066112002086
ovaryDCP2chr5112345642112345662DCP2chr5112342280112342300
pancreasDCP2chr5112332702112332722SRP19chr5112224571112224591
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DCP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK025019KLF1126121019381910193878DCP26125115112354215112356667
CA945240DCP212205112356465112357100DCP22133085112356368112356463
CB852569DCP2212265112320135112320344DCP22213695112320003112320151

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=34)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr5:112327832-112327832p.P74T2
chr5:112337369-112337369p.L268L2
chr5:112336808-112336808p.K154E2
chr5:112339641-112339641p.R270Q2
chr5:112346489-112346489p.D362Y2
chr5:112321534-112321534p.R19Q2
chr5:112321592-112321592p.Q38H1
chr5:112343660-112343660p.R323K1
chr5:112328440-112328440p.E135D1
chr5:112349069-112349069p.A384D1

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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
# sample2  7  1    1   156 13
# mutation2  7  1    1   156 13
nonsynonymous SNV2  5  1        144 10
synonymous SNV   2       1    12 3
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
chr5:112327826p.P74S,DCP21
chr5:112337070p.L268L,DCP21
chr5:112343646p.P74P,DCP21
chr5:112327832p.R270L,DCP21
chr5:112337129p.Q79E,DCP21
chr5:112343651p.R274H,DCP21
chr5:112327834p.V115I,DCP21
chr5:112337142p.Q277Q,DCP21
chr5:112343668p.K133T,DCP21
chr5:112327847p.H304Y,DCP21

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 DCP2 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 DCP2

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

APC,C5orf24,CSNK1G3,DCP2,DMXL1,ERBB2IP,FAM13B,
LYSMD3,MATR3,MFAP3,MIER3,PPIP5K2,RBM27,SAP30L,
SLC25A46,SMAD5,SRFBP1,TNPO1,TRIM23,WDR36,YTHDC2
CNOT6,DCP2,LSM11,RBM12B,SPIN4,TRIM59,ZBTB33,
ZFP14,ZFP62,ZNF223,ZNF235,ZNF253,ZNF260,ZNF264,
ZNF286A,ZNF525,ZNF529,ZNF681,ZNF709,ZNF780A,ZNF84

ANKRD32,APC,BDP1,CEP120,CHD1,CNOT6,DCP2,
DDX46,DMXL1,FBXW11,FER,GXYLT1,NSD1,PHAX,
PIKFYVE,SRP19,TRIM23,WDFY2,WDR36,YTHDC2,ZFYVE16
AIM1,CSNK1G1,CSNK2A1,DCP2,DNMT3B,FAM117B,HARS2,
KDM4A,NAPEPLD,NLK,OSBP,PANK2,SPG11,SPTLC2,
STK4,STRBP,TAF5,VCPIP1,WDFY1,ZNF217,ZNF490
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 DCP2


There's no related Drug.
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Cross referenced IDs for DCP2
* 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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