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 DDX20
Basic gene info.Gene symbolDDX20
Gene nameDEAD (Asp-Glu-Ala-Asp) box polypeptide 20
SynonymsDP103|GEMIN3
CytomapUCSC genome browser: 1p21.1-p13.2
Genomic locationchr1 :112298189-112310199
Type of geneprotein-coding
RefGenesNM_007204.4,
Ensembl idENSG00000064703
DescriptionDEAD box protein 20DEAD box protein DP 103DEAD-box protein DP103DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kDSMN-interacting proteincomponent of gems 3gemin-3probable ATP-dependent RNA helicase DDX20
Modification date20141207
dbXrefs MIM : 606168
HGNC : HGNC
Ensembl : ENSG00000064703
HPRD : 05859
Vega : OTTHUMG00000011956
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDX20
BioGPS: 11218
Gene Expression Atlas: ENSG00000064703
The Human Protein Atlas: ENSG00000064703
PathwayNCI Pathway Interaction Database: DDX20
KEGG: DDX20
REACTOME: DDX20
ConsensusPathDB
Pathway Commons: DDX20
MetabolismMetaCyc: DDX20
HUMANCyc: DDX20
RegulationEnsembl's Regulation: ENSG00000064703
miRBase: chr1 :112,298,189-112,310,199
TargetScan: NM_007204
cisRED: ENSG00000064703
ContextiHOP: DDX20
cancer metabolism search in PubMed: DDX20
UCL Cancer Institute: DDX20
Assigned class in ccmGDBC

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Phenotypic Information for DDX20(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DDX20
Familial Cancer Database: DDX20
* 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_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DDX20
MedGen: DDX20 (Human Medical Genetics with Condition)
ClinVar: DDX20
PhenotypeMGI: DDX20 (International Mouse Phenotyping Consortium)
PhenomicDB: DDX20

Mutations for DDX20
* 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
ovaryDDX20chr1112299278112299298DDX20chr1112299560112299580
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 DDX20 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
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=45)
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
chr1:112298570-112298570p.S8S4
chr1:112304906-112304906p.A351S3
chr1:112308673-112308673p.E543K3
chr1:112309217-112309217p.K724I2
chr1:112308533-112308533p.S496F2
chr1:112308652-112308652p.L536L2
chr1:112308952-112308952p.I636V2
chr1:112298829-112298829p.L95L2
chr1:112303389-112303389p.E248K2
chr1:112308972-112308972p.V642V2

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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
# sample32 81 6 42 3    74 7
# mutation32 91 6 43 3    74 7
nonsynonymous SNV22 51 3 33 2    54 5
synonymous SNV1  4  3 1  1    2  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
chr1:112308673p.E543K3
chr1:112303389p.E248K2
chr1:112308658p.C538R2
chr1:112308375p.L200L1
chr1:112303111p.A426V1
chr1:112308795p.Y587C1
chr1:112305328p.I431V1
chr1:112309315p.E607D1
chr1:112308378p.V292A1
chr1:112303130p.P435P1

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 DDX20 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 DDX20

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

ATP5F1,CAPZA1,CLCC1,CSDE1,DDX20,DNTTIP2,GLMN,
GNAI3,LRIG2,PKN2,PRPF38B,RAP1A,RBMXL1,RPAP2,
RSBN1,SASS6,SIKE1,STXBP3,WDR77,ZNF326,ZNF644
API5,COIL,DDX20,GABPB1,LAMTOR3,NOL11,NUP35,
PACRGL,POT1,TADA1,TMEM123,TTC19,TWISTNB,WDR89,
ZBED5,ZNF140,ZNF146,ZNF184,ZNF195,ZNF567,ZNF627

ATP5F1,BCAS2,COA7,TRMT13,CEPT1,DCLRE1B,DDX20,
DNTTIP2,GLMN,LRRC8D,MTF2,PSMA5,TRMT10C,RPAP2,
SASS6,SERBP1,SIKE1,STXBP3,TTF2,WDR3,WDR77
ALDH1B1,TPGS2,DBR1,DCLRE1B,DDX20,DSE,FAM175B,
FIGNL1,FTSJ2,IPO11,LOC339524,MCPH1,NOL11,NUP160,
OGFOD1,RBMXL1,SF3A3,SRRD,TEX10,TRMT5,USP1
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 DDX20


There's no related Drug.
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Cross referenced IDs for DDX20
* 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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