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 DCP1B
Basic gene info.Gene symbolDCP1B
Gene namedecapping mRNA 1B
SynonymsDCP1|hDcp1b
CytomapUCSC genome browser: 12p13.33
Genomic locationchr12 :2055213-2113677
Type of geneprotein-coding
RefGenesNM_152640.3,
Ensembl idENSG00000151065
DescriptionDCP1 decapping enzyme homolog Bdecapping enzyme hDcp1bmRNA-decapping enzyme 1B
Modification date20141207
dbXrefs MIM : 609843
HGNC : HGNC
Ensembl : ENSG00000151065
Vega : OTTHUMG00000168113
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DCP1B
BioGPS: 196513
Gene Expression Atlas: ENSG00000151065
The Human Protein Atlas: ENSG00000151065
PathwayNCI Pathway Interaction Database: DCP1B
KEGG: DCP1B
REACTOME: DCP1B
ConsensusPathDB
Pathway Commons: DCP1B
MetabolismMetaCyc: DCP1B
HUMANCyc: DCP1B
RegulationEnsembl's Regulation: ENSG00000151065
miRBase: chr12 :2,055,213-2,113,677
TargetScan: NM_152640
cisRED: ENSG00000151065
ContextiHOP: DCP1B
cancer metabolism search in PubMed: DCP1B
UCL Cancer Institute: DCP1B
Assigned class in ccmGDBC

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Phenotypic Information for DCP1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DCP1B
Familial Cancer Database: DCP1B
* 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: DCP1B
MedGen: DCP1B (Human Medical Genetics with Condition)
ClinVar: DCP1B
PhenotypeMGI: DCP1B (International Mouse Phenotyping Consortium)
PhenomicDB: DCP1B

Mutations for DCP1B
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryDCP1Bchr1220655962065616FLJ35024chr925857592585779
ovaryDCP1Bchr1220990032099023DCP1Bchr1220980112098031
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 DCP1B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW262847PPP5C170194689403946894108DCP1B603321220622512064666

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 # sample2     1         2
GAIN (# sample)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=18

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=49)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=8)
There's no deleted 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
chr12:2062350-2062350p.Q252H18
chr12:2102455-2102455p.P98P6
chr12:2062323-2062324p.Q261_E262insQ4
chr12:2062038-2062038p.F356F4
chr12:2062353-2062354p.H251_Q252insG3
chr12:2061728-2061728p.Q460*2
chr12:2061671-2061671p.V479M2
chr12:2061889-2061889p.A406D1
chr12:2062241-2062241p.Q289*1
chr12:2058419-2058419p.V536I1

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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
# sample21 6  3  1  61  43 6
# mutation21 6  3  1  61  44 6
nonsynonymous SNV2  5  3  1  6   24 3
synonymous SNV 1 1         1  2  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
chr12:2062038p.F356F3
chr12:2113469p.F43L1
chr12:2058478p.Q463K1
chr12:2062114p.I31I1
chr12:2113505p.Q426Q1
chr12:2058485p.M617V1
chr12:2062288p.R384C1
chr12:2055377p.N383H1
chr12:2061665p.I599V1
chr12:2062350p.I564V1

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 DCP1B 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 DCP1B

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

ATN1,RHNO1,C17orf97,RRNAD1,COPS7A,DCP1B,DYRK4,
EMG1,FBXL14,FKBP4,ING4,ITFG2,KLHDC9,LOC678655,
MLF2,PEX5,PHB2,PHC1,RAD52,TCTN1,ZNF384
APOBEC3F,BCDIN3D,RHNO1,C12orf76,C17orf100,DCP1B,GSTO2,
IRX2,LOC642587,MORN4,PATZ1,POC5,PRR3,RBM4B,
REPS1,SRSF8,TBP,TRAPPC2,VGLL4,ZNF211,ZNF346

ADIPOR2,B4GALNT3,RHNO1,C12orf5,CACNA1C,CCDC77,CCND2,
CHRNA6,DCP1B,CRACR2A,FBXL14,FKBP4,FOXM1,GPR139,
IFNA13,ITFG2,NKX6-3,OR9K2,PARP11,TEAD4,TULP3
ABHD8,BEND5,C3orf18,CLUAP1,DCP1B,DPF2,HLX,
KLHDC8B,KLHL22,LOC441869,LZTS2,PGM5P2,PHLDA3,RBM43,
RRAS,RTN2,SNAPC2,THAP8,TRAM1L1,TSPY26P,ZNF174
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 DCP1B
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
DB00184decapping mRNA 1BapprovedNicotine


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Cross referenced IDs for DCP1B
* 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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