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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for XRCC4
check button Gene summary
Basic gene informationGene symbolXRCC4
Gene nameX-ray repair complementing defective repair in Chinese hamster cells 4
Synonyms-
CytomapUCSC genome browser: 5q14.2
Type of geneprotein-coding
RefGenesNM_003401.3,
NM_022406.2,NM_022550.2,
DescriptionDNA repair protein XRCC4X-ray repair cross-complementing protein 4X-ray repair, complementing defective, repair in Chinese hamster
Modification date20141222
dbXrefs MIM : 194363
HGNC : HGNC
Ensembl : ENSG00000152422
HPRD : 15951
Vega : OTTHUMG00000131319
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XRCC4
BioGPS: 7518
PathwayNCI Pathway Interaction Database: XRCC4
KEGG: XRCC4
REACTOME: XRCC4
Pathway Commons: XRCC4
ContextiHOP: XRCC4
ligand binding site mutation search in PubMed: XRCC4
UCL Cancer Institute: XRCC4
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Bone marrowTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LAMLTGCT
Reference showing the relevant tissue of XRCC4
Description by TissGene annotationsCancer gene
TissgsLTS
* 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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0006302double-strand break repair9242410
GO:0006303double-strand break repair via nonhomologous end joining12517771
GO:0010165response to X-ray9242410
GO:0051103DNA ligation involved in DNA repair12517771
GO:0051351positive regulation of ligase activity9242410
GO:0006302double-strand break repair9242410
GO:0006303double-strand break repair via nonhomologous end joining12517771
GO:0010165response to X-ray9242410
GO:0051103DNA ligation involved in DNA repair12517771
GO:0051351positive regulation of ligase activity9242410


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TissGeneExp for XRCC4

check button 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 exp


check button 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 isoform exp


check button 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.
normal gene exp


check button 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)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR


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TissGene-miRNA for XRCC4

check button 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 typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for XRCC4
TissGeneSNV for XRCC4

check button 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.
SNV lollipop
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check button 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)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.M319TTHYM1
p.L10FSKCM1
p.L152PSTAD1
p.M61TCOAD1
p.H195RLIHC1
p.K146NLIHC1
p.L319SLUAD1
p.R225QBLCA1
p.R275QBRCA1
p.P14ASKCM1
p.S248LBLCA1
p.Q289HSTAD1
p.R7IUCEC1
p.D230NBRCA1
p.L144PCOAD1
p.D157NBLCA1
p.A60TUCEC1
p.F86LUCEC1
p.I16KSTAD1
p.G109VLUAD1
p.E125XREAD1
p.R272SBLCA1
p.E220QBRCA1
p.R179WKICH1
p.W24SHNSC1
p.S303YCOAD1
p.S53FSKCM1
p.Q289HLUAD1
p.N141THNSC1
p.S12CDLBC1
p.R275XTHYM1
p.H143RSTAD1
p.L36PUCEC1


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TissGeneCNV for XRCC4

check button 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)
CNV


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TissGeneFusions for XRCC4

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNABG282107TPD52L2-XRCC4chr20:62522725chr5:82648950
TCGAfusionPortalPRADALUSCTCGA-43-3920-01ACOL4A5-XRCC4Out-of-frameChrX:107683436Chr5:82648944


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TissGeneNet for XRCC4

check button 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)
BRCA (tumor)BRCA (normal)
XRCC4, CSNK2A1, XRCC5, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, XRCC6, APTX, GZMB, NHEJ1 (normal)
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COAD (tumor)COAD (normal)
XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, PRKDC, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, GORAB, LIG4, SETMAR, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (normal)
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HNSC (tumor)HNSC (normal)
XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PNKP, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (normal)
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KICH (tumor)KICH (normal)
XRCC4, CSNK2A1, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, BIN1, NBN, GORAB, LIG4, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (normal)
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KIRC (tumor)KIRC (normal)
XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, SETMAR, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, SUMO2, CHD3, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, NHEJ1 (normal)
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KIRP (tumor)KIRP (normal)
XRCC4, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB (normal)
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LIHC (tumor)LIHC (normal)
XRCC4, HNF4A, XRCC5, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APTX, IFFO1, GZMB, NHEJ1 (normal)
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LUAD (tumor)LUAD (normal)
XRCC4, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, VIM, XRCC6, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (normal)
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LUSC (tumor)LUSC (normal)
XRCC4, CSNK2A1, XRCC5, UBC, SUMO2, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, XRCC5, SUMO2, CHD3, AHNAK, CALM1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (normal)
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PRAD (tumor)PRAD (normal)
XRCC4, CSNK2A1, HNF4A, XRCC5, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, SETMAR, PRKDC, PNKP, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, XRCC5, SUMO2, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (normal)
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STAD (tumor)STAD (normal)
XRCC4, HNF4A, XRCC5, UBC, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APLF, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, UBC, SUMO2, CHD3, AHNAK, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, VIM, APLF, APTX, IFFO1, GZMB (normal)
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THCA (tumor)THCA (normal)
XRCC4, CSNK2A1, XRCC5, UBC, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, SETMAR, PRKDC, PNKP, ACTN1, VIM, XRCC6, APTX, IFFO1, GZMB, NHEJ1 (tumor)XRCC4, CSNK2A1, HNF4A, XRCC5, SUMO2, CHD3, AHNAK, CALM1, BIN1, NBN, GORAB, LIG4, SETMAR, PRKDC, PNKP, ACTN1, XRCC6, APLF, APTX, GZMB, NHEJ1 (normal)
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TissGeneProg for XRCC4

check button 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.
survival 1

check button 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.
survival 2

check button 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.
survival 3

check button 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.
survival 4

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TissGeneClin for XRCC4
TissGeneDrug for XRCC4

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for XRCC4

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0006142Malignant neoplasm of breast12BeFree,GAD
umls:C0596263Carcinogenesis11BeFree
umls:C0678222Breast Carcinoma10BeFree
umls:C0005684Malignant neoplasm of urinary bladder6BeFree,GAD
umls:C0017638Glioma5BeFree,GAD
umls:C0242379Malignant neoplasm of lung5BeFree,GAD
umls:C0026640Mouth Neoplasms4GAD,LHGDN
umls:C0153381Malignant neoplasm of mouth4BeFree
umls:C0220641Lip and Oral Cavity Carcinoma4BeFree
umls:C0006118Brain Neoplasms3GAD
umls:C0007131Non-Small Cell Lung Carcinoma3BeFree
umls:C0013336Dwarfism3BeFree
umls:C0026764Multiple Myeloma3BeFree,GAD
umls:C0038356Stomach Neoplasms3GAD,LHGDN
umls:C0376358Malignant neoplasm of prostate3BeFree,GAD
umls:C0699885Carcinoma of bladder3BeFree
umls:C2239176Liver carcinoma3BeFree
umls:C0007137Squamous cell carcinoma2GAD
umls:C0008626Congenital chromosomal disease2BeFree
umls:C0009402Colorectal Carcinoma2BeFree
umls:C0023418leukemia2BeFree,GAD
umls:C0024299Lymphoma2BeFree
umls:C0024301Lymphoma, Follicular2BeFree,GAD
umls:C0040136Thyroid Neoplasm2GAD
umls:C0342573PITUITARY DWARFISM I2BeFree,CLINVAR
umls:C0600139Prostate carcinoma2BeFree
umls:C0684249Carcinoma of lung2BeFree
umls:C1458155Mammary Neoplasms2GAD,LHGDN
umls:C1527249Colorectal Cancer2BeFree,GAD
umls:C0001418Adenocarcinoma1BeFree,GAD
umls:C0001486Adenovirus Infections1BeFree
umls:C0001973Alcoholic Intoxication, Chronic1BeFree
umls:C0003873Rheumatoid Arthritis1BeFree
umls:C0007133Carcinoma, Papillary1GAD
umls:C0007134Renal Cell Carcinoma1LHGDN
umls:C0008625Chromosome Aberrations1CTD_human
umls:C0009404Colorectal Neoplasms1GAD
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent1GAD
umls:C0012860DNA Damage1GAD
umls:C0014175Endometriosis1BeFree,GAD,LHGDN
umls:C0015544Failure to Thrive1BeFree
umls:C0015625Fanconi Anemia1BeFree
umls:C0020538Hypertensive disease1GWASCAT
umls:C0023267Fibroid Tumor1BeFree,GAD
umls:C0023434Chronic Lymphocytic Leukemia1GAD
umls:C0023895Liver diseases1BeFree
umls:C0024117Chronic Obstructive Airway Disease1GAD
umls:C0024305Lymphoma, Non-Hodgkin1BeFree,GAD
umls:C0024623Malignant neoplasm of stomach1BeFree,GAD
umls:C0025284Meningeal Neoplasms1GAD
umls:C0025286Meningioma1GAD
umls:C0026769Multiple Sclerosis1GAD
umls:C0027086Myoma1BeFree
umls:C0027819Neuroblastoma1BeFree
umls:C0027859Acoustic Neuroma1GAD
umls:C0032927Precancerous Conditions1GAD
umls:C0036341Schizophrenia1BeFree,GAD
umls:C0036421Systemic Scleroderma1BeFree
umls:C0039101synovial sarcoma1BeFree
umls:C0042133Uterine Fibroids1BeFree
umls:C0079744Diffuse Large B-Cell Lymphoma1GAD
umls:C0079745Lymphoma, Large-Cell, Follicular1BeFree
umls:C0085110Severe Combined Immunodeficiency1BeFree
umls:C0268138Xeroderma Pigmentosum, Complementation Group D1BeFree
umls:C02686155,10-Methylenetetrahydrofolate reductase deficiency1BeFree
umls:C0279000Liver and Intrahepatic Biliary Tract Carcinoma1BeFree
umls:C0345904Malignant neoplasm of liver1BeFree
umls:C0518010body mass1GAD
umls:C0524620Metabolic Syndrome X1BeFree
umls:C0677886Epithelial ovarian cancer1GAD
umls:C0699791Stomach Carcinoma1BeFree
umls:C0850666Helicobacter pylori infection1BeFree
umls:C0878787Growth failure1BeFree
umls:C3469521FANCONI ANEMIA, COMPLEMENTATION GROUP A (disorder)1BeFree
umls:C3539878Triple Negative Breast Neoplasms1BeFree