TissGeneSummary for DDX4 |
Gene summary |
Basic gene information | Gene symbol | DDX4 |
Gene name | DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 | |
Synonyms | VASA | |
Cytomap | UCSC genome browser: 5p15.2-p13.1 | |
Type of gene | protein-coding | |
RefGenes | NM_019039.1, NM_001142549.1,NM_001166533.1,NM_001166534.1,NM_024415.2, | |
Description | DEAD box protein 4DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4probable ATP-dependent RNA helicase DDX4vasa homolog | |
Modification date | 20141207 | |
dbXrefs | MIM : 605281 | |
HGNC : HGNC | ||
Ensembl : ENSG00000152670 | ||
HPRD : 05593 | ||
Vega : OTTHUMG00000097044 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_DDX4 | |
BioGPS: 54514 | ||
Pathway | NCI Pathway Interaction Database: DDX4 | |
KEGG: DDX4 | ||
REACTOME: DDX4 | ||
Pathway Commons: DDX4 | ||
Context | iHOP: DDX4 | |
ligand binding site mutation search in PubMed: DDX4 | ||
UCL Cancer Institute: DDX4 | ||
Assigned class in TissGDB* | A | |
Included tissue-specific gene expression resources | HPA,TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Testis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
Reference showing the relevant tissue of DDX4 | Identification of cell-specific targets of sumoylation during mouse spermatogenesis. Xiao Y, Pollack D, Andrusier M, Levy A, Callaway M, Nieves E, Reddi P, Vigodner M. Reproduction. 2016 Feb;151(2):149-66. doi: 10.1530/REP-15-0239. (pmid:26701181) go to article | |
Description by TissGene annotations | High usage of specific isoform TissgsKTS |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for DDX4 |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
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TissGene-miRNA for DDX4 |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
THYM | hsa-miR-373-3p | MIMAT0000726 | 0.029 | -0.26 | 122 |
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TissGeneMut for DDX4 |
TissGeneSNV for DDX4 |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.R410* | UCEC | 2 |
p.R123W | BLCA | 2 |
p.R587C | SKCM | 2 |
p.S471X | STAD | 1 |
p.A293V | STAD | 1 |
p.R395I | UCEC | 1 |
p.M55I | SKCM | 1 |
p.A332T | HNSC | 1 |
p.S694L | BLCA | 1 |
p.G159A | LUAD | 1 |
p.D170E | BLCA | 1 |
p.G62V | LUAD | 1 |
p.A260S | THYM | 1 |
p.G66E | SKCM | 1 |
p.G31A | BRCA | 1 |
p.K527Q | PAAD | 1 |
p.F555V | UCS | 1 |
p.S648L | ESCA | 1 |
p.E118K | UCEC | 1 |
p.D307Y | COAD | 1 |
p.M469I | SKCM | 1 |
p.R627L | THYM | 1 |
p.R147G | LUSC | 1 |
p.V659L | PAAD | 1 |
p.G382V | COAD | 1 |
p.P124L | LGG | 1 |
p.G136E | SARC | 1 |
p.S106R | STAD | 1 |
p.A582T | SKCM | 1 |
p.R450H | UCEC | 1 |
p.R134* | SKCM | 1 |
p.E459K | BLCA | 1 |
p.N11T | OV | 1 |
p.R326* | THCA | 1 |
p.F588I | ESCA | 1 |
p.S142* | BLCA | 1 |
p.E216K | SKCM | 1 |
p.P592T | LUSC | 1 |
p.R536Q | UCEC | 1 |
p.R536G | BLCA | 1 |
p.F109I | OV | 1 |
p.S566L | BLCA | 1 |
p.P144L | LGG | 1 |
p.S97* | PAAD | 1 |
p.G195S | LUAD | 1 |
p.D616V | UCEC | 1 |
p.G83C | LUAD | 1 |
p.P668S | SKCM | 1 |
p.D696Y | LUAD | 1 |
p.V505A | STAD | 1 |
p.R375Q | SKCM | 1 |
p.E533K | SKCM | 1 |
p.P250H | STAD | 1 |
p.N294D | LIHC | 1 |
p.R68K | HNSC | 1 |
p.S471* | STAD | 1 |
p.F390C | UCEC | 1 |
p.E43D | READ | 1 |
p.V371L | LGG | 1 |
p.R177H | UCS | 1 |
p.V659L | UCEC | 1 |
p.E575A | BLCA | 1 |
p.P681S | KICH | 1 |
p.I430M | UCEC | 1 |
p.A601T | SKCM | 1 |
p.V532I | STAD | 1 |
p.S61F | BRCA | 1 |
p.R450L | KIRP | 1 |
p.W6* | SKCM | 1 |
p.G139X | COAD | 1 |
p.V444I | OV | 1 |
p.F480L | UCEC | 1 |
p.K442X | THCA | 1 |
p.R410* | LGG | 1 |
p.E292* | STAD | 1 |
p.E72D | LUAD | 1 |
p.R50Q | ACC | 1 |
p.Y271* | SKCM | 1 |
p.S648L | SKCM | 1 |
p.K530Q | UCEC | 1 |
p.R157H | LGG | 1 |
p.M82L | PAAD | 1 |
p.L463* | SKCM | 1 |
p.G95C | STAD | 1 |
p.S498L | BRCA | 1 |
p.R610H | KIRP | 1 |
p.C393Y | KIRC | 1 |
p.K270N | UCS | 1 |
p.P648S | SKCM | 1 |
p.R567C | SKCM | 1 |
p.G509V | LUAD | 1 |
p.K441T | STAD | 1 |
p.K361E | BLCA | 1 |
p.V667A | UCEC | 1 |
p.D234N | SKCM | 1 |
p.D254N | SKCM | 1 |
p.S648L | HNSC | 1 |
p.A600S | SARC | 1 |
p.H13Y | BLCA | 1 |
p.R375* | UCEC | 1 |
p.D46N | KIRC | 1 |
p.G180D | PAAD | 1 |
p.A714T | UCEC | 1 |
p.P485L | LUAD | 1 |
p.R326* | LUAD | 1 |
p.D327Y | UCEC | 1 |
p.T356A | SKCM | 1 |
p.R123L | ACC | 1 |
p.R630H | KIRP | 1 |
p.E9K | SKCM | 1 |
p.V691M | LIHC | 1 |
p.A348V | LIHC | 1 |
p.D540N | SKCM | 1 |
p.L443X | SKCM | 1 |
p.E487K | SKCM | 1 |
p.D196N | SKCM | 1 |
p.Y624H | HNSC | 1 |
p.P458L | STAD | 1 |
p.K462* | THCA | 1 |
p.R123W | LGG | 1 |
p.Q199* | BLCA | 1 |
p.E494* | UCEC | 1 |
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TissGeneCNV for DDX4 |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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TissGeneFusions for DDX4 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
TCGAfusionPortal | PRADA | BRCA | TCGA-E9-A228-01A | KAT6B-DDX4 | CDS-5UTR | Chr10:76748870 | Chr5:55034778 |
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TissGeneNet for DDX4 |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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TissGeneProg for DDX4 |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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TissGeneClin for DDX4 |
TissGeneDrug for DDX4 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for DDX4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0004509 | Azoospermia | 1 | BeFree |
umls:C0013377 | Dysgerminoma | 1 | BeFree |
umls:C0014145 | Yolk Sac Tumor | 1 | BeFree |
umls:C0021364 | Male infertility | 1 | BeFree |
umls:C0023601 | Leydig Cell Tumor | 1 | BeFree |
umls:C0024299 | Lymphoma | 1 | BeFree |
umls:C0027819 | Neuroblastoma | 1 | BeFree,GAD |
umls:C0028960 | Oligospermia | 1 | BeFree |
umls:C0036631 | Seminoma | 1 | BeFree |
umls:C0205851 | Germ cell tumor | 1 | BeFree |
umls:C0206659 | Embryonal Carcinoma | 1 | BeFree |
umls:C0206661 | Gonadoblastoma | 1 | BeFree |
umls:C0334409 | Leydig cell tumor, benign | 1 | BeFree |
umls:C0334517 | Spermatocytic seminoma | 1 | BeFree |
umls:C0403814 | Congenital bilateral aplasia of vas deferens | 1 | BeFree |
umls:C0596263 | Carcinogenesis | 1 | BeFree |
umls:C0677886 | Epithelial ovarian cancer | 1 | BeFree |
umls:C0700095 | Central neuroblastoma | 1 | BeFree |
umls:C0919267 | ovarian neoplasm | 1 | LHGDN |
umls:C1266158 | Nonseminomatous germ cell tumor | 1 | BeFree |