Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 DDX6
Basic gene info.Gene symbolDDX6
Gene nameDEAD (Asp-Glu-Ala-Asp) box helicase 6
SynonymsHLR2|P54|RCK
CytomapUCSC genome browser: 11q23.3
Genomic locationchr11 :118618472-118661972
Type of geneprotein-coding
RefGenesNM_001257191.2,
NM_004397.5,
Ensembl idENSG00000269612
DescriptionATP-dependent RNA helicase p54DEAD (Asp-Glu-Ala-Asp) box polypeptide 6DEAD box protein 6DEAD box-6DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)oncogene RCKprobable ATP-dependent RNA helicase DDX6
Modification date20141207
dbXrefs MIM : 600326
HGNC : HGNC
Ensembl : ENSG00000110367
HPRD : 02638
ProteinUniProt: P26196
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDX6
BioGPS: 1656
Gene Expression Atlas: ENSG00000269612
The Human Protein Atlas: ENSG00000269612
PathwayNCI Pathway Interaction Database: DDX6
KEGG: DDX6
REACTOME: DDX6
ConsensusPathDB
Pathway Commons: DDX6
MetabolismMetaCyc: DDX6
HUMANCyc: DDX6
RegulationEnsembl's Regulation: ENSG00000269612
miRBase: chr11 :118,618,472-118,661,972
TargetScan: NM_001257191
cisRED: ENSG00000269612
ContextiHOP: DDX6
cancer metabolism search in PubMed: DDX6
UCL Cancer Institute: DDX6
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DDX6 in cancer cell metabolism1. Iio A, Takagi T, Miki K, Naoe T, Nakayama A, et al. (2013) DDX6 post-transcriptionally down-regulates miR-143/145 expression through host gene NCR143/145 in cancer cells. Biochim Biophys Acta 1829: 1102-1110. doi: 10.1016/j.bbagrm.2013.07.010. go to article

Top
Phenotypic Information for DDX6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DDX6
Familial Cancer Database: DDX6
* 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 600326; gene.
Orphanet
DiseaseKEGG Disease: DDX6
MedGen: DDX6 (Human Medical Genetics with Condition)
ClinVar: DDX6
PhenotypeMGI: DDX6 (International Mouse Phenotyping Consortium)
PhenomicDB: DDX6

Mutations for DDX6
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryDDX6chr11118652817118652837LNX2chr132812023728120257
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 DDX6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC065007DDX625251511118622042118657228RAB7A250625683128533579128533641
BF085678DDX6642911118635822118636246C14orf37424576145876027658760429
BF356738DDX6115711118647776118647931FGD4153431123269948732699765
BE934709DDX6116311118622197118622362DDX615823011118618929118619001
DN997510DDX6845711118656818118661846ROBO143845737876660378766622

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          1      
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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr11:118626197-118626197p.G386D3
chr11:118626210-118626210p.L382M2
chr11:118630698-118630698p.T255M2
chr11:118627025-118627025p.R362Q2
chr11:118627889-118627889p.K356K2
chr11:118633946-118633946p.H228R1
chr11:118625512-118625512p.G443E1
chr11:118650398-118650398p.K93K1
chr11:118627891-118627891p.K356E1
chr11:118633979-118633979p.D217G1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 81 3 4  111  13 5
# mutation12 71 3 4  111  13 6
nonsynonymous SNV12 51 2 2   11   1 4
synonymous SNV   2  1 2  1    12 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])

Top
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
chr11:118626210p.L393L,DDX62
chr11:118627889p.K367K,DDX62
chr11:118639000p.R443C,DDX61
chr11:118625512p.L229I,DDX61
chr11:118629524p.Q401H,DDX61
chr11:118650341p.G192G,DDX61
chr11:118625546p.I400L,DDX61
chr11:118629570p.R157W,DDX61
chr11:118650398p.G397D,DDX61
chr11:118626184p.I152S,DDX61

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 DDX6 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]

Top
Gene Expression for DDX6

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ARCN1,ARHGEF12,ATM,BCLAF1,CCDC186,C11orf57,CBL,
CREB1,CUL5,DDX6,DLAT,MGA,KMT2A,NPAT,
PAFAH1B2,PRDM10,RBM7,TBCEL,UBE4A,USP28,ZW10
ARIH1,ASH1L,BTBD7,BROX,DDX6,GSK3B,IPO8,
KIAA0430,NR2C2,NUCKS1,PREPL,RAB3GAP2,TAB2,TMEM184C,
TNKS,USP34,USP48,XPO7,ZFX,ZMYM4,ZNF510

ARCN1,ARHGEF12,C11orf30,CBL,DDX6,HIPK3,KDM2A,
KIAA0430,KMT2A,NPAT,PICALM,PRDM10,REV3L,RNF169,
RSF1,SON,SOS1,TRIP11,UBE4A,USP34,ZBTB44
ARID2,COL4A3BP,DDX6,DYNLL2,DYRK1A,FBXO11,FBXW11,
GLG1,HNRNPUL2,IPO8,JAK1,KIF1B,MAPK1,PAFAH1B1,
PHF3,PIK3R4,SEL1L,SMG7,TNRC6B,USP9X,ZC3HAV1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for DDX6
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA27229; -.
Organism-specific databasesCTD 1656; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01694DEAD (Asp-Glu-Ala-Asp) box helicase 6experimentalD-tartaric acid


Top
Cross referenced IDs for DDX6
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas