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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 NKX3-1
check button Gene summary
Basic gene informationGene symbolNKX3-1
Gene nameNK3 homeobox 1
SynonymsBAPX2|NKX3|NKX3.1|NKX3A
CytomapUCSC genome browser: 8p21.2
Type of geneprotein-coding
RefGenesNM_001256339.1,
NM_006167.3,NR_046072.1,
DescriptionNK homeobox, family 3, ANK3 transcription factor homolog ANK3 transcription factor related, locus 1homeobox protein NK-3 homolog Ahomeobox protein Nkx-3.1
Modification date20141222
dbXrefs MIM : 602041
HGNC : HGNC
Ensembl : ENSG00000167034
HPRD : 03620
Vega : OTTHUMG00000097851
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NKX3-1
BioGPS: 4824
PathwayNCI Pathway Interaction Database: NKX3-1
KEGG: NKX3-1
REACTOME: NKX3-1
Pathway Commons: NKX3-1
ContextiHOP: NKX3-1
ligand binding site mutation search in PubMed: NKX3-1
UCL Cancer Institute: NKX3-1
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Prostate
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)PRAD
Reference showing the relevant tissue of NKX3-1Chromosome 8 markers of metastatic prostate cancer in African American men: gain of the MIR151 gene and loss of the NKX3-1 gene. Barnabas N, Xu L, Savera A, Hou Z, Barrack ER. Prostate. 2011 Jun 1;71(8):857-71. doi: 10.1002/pros.21302. Epub 2010 Nov 17 (pmid:21456068)
go to article
Description by TissGene annotationsProtective TissGene in RFS
Cancer gene
TissgsKTS
CNV lost TissGeneKTS
* 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:0001934positive regulation of protein phosphorylation20395202
GO:0006919activation of cysteine-type endopeptidase activity involved in apoptotic process17486276
GO:0008285negative regulation of cell proliferation17486276
GO:0010628positive regulation of gene expression17486276
GO:0010629negative regulation of gene expression17486276
GO:0010942positive regulation of cell death19266349
GO:0014068positive regulation of phosphatidylinositol 3-kinase signaling20395202
GO:0030521androgen receptor signaling pathway19886863
GO:0043280positive regulation of cysteine-type endopeptidase activity involved in apoptotic process20599703
GO:0043401steroid hormone mediated signaling pathway18794125
GO:0045860positive regulation of protein kinase activity20395202
GO:0045892negative regulation of transcription, DNA-templated18794125
GO:0045930negative regulation of mitotic cell cycle19266349
GO:0045944positive regulation of transcription from RNA polymerase II promoter19797053
GO:0071383cellular response to steroid hormone stimulus19886863
GO:0071456cellular response to hypoxia21056661
GO:0071850mitotic cell cycle arrest19266349
GO:0071899negative regulation of estrogen receptor binding18794125
GO:2000836positive regulation of androgen secretion19886863
GO:2001022positive regulation of response to DNA damage stimulus20395202
GO:2001235positive regulation of apoptotic signaling pathway20599703
GO:2001244positive regulation of intrinsic apoptotic signaling pathway17486276
GO:0001934positive regulation of protein phosphorylation20395202
GO:0006919activation of cysteine-type endopeptidase activity involved in apoptotic process17486276
GO:0008285negative regulation of cell proliferation17486276
GO:0010628positive regulation of gene expression17486276
GO:0010629negative regulation of gene expression17486276
GO:0010942positive regulation of cell death19266349
GO:0014068positive regulation of phosphatidylinositol 3-kinase signaling20395202
GO:0030521androgen receptor signaling pathway19886863
GO:0043280positive regulation of cysteine-type endopeptidase activity involved in apoptotic process20599703
GO:0043401steroid hormone mediated signaling pathway18794125
GO:0045860positive regulation of protein kinase activity20395202
GO:0045892negative regulation of transcription, DNA-templated18794125
GO:0045930negative regulation of mitotic cell cycle19266349
GO:0045944positive regulation of transcription from RNA polymerase II promoter19797053
GO:0071383cellular response to steroid hormone stimulus19886863
GO:0071456cellular response to hypoxia21056661
GO:0071850mitotic cell cycle arrest19266349
GO:0071899negative regulation of estrogen receptor binding18794125
GO:2000836positive regulation of androgen secretion19886863
GO:2001022positive regulation of response to DNA damage stimulus20395202
GO:2001235positive regulation of apoptotic signaling pathway20599703
GO:2001244positive regulation of intrinsic apoptotic signaling pathway17486276


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TissGeneExp for NKX3-1

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)

- 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 NKX3-1

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 NKX3-1
TissGeneSNV for NKX3-1

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.H133PPRAD1
p.X235QKICH1
p.R128QUCEC1
p.N215SUCEC1
p.P218SSKCM1
p.S110*LUAD1
p.P231LSKCM1
p.K147NLUAD1
p.E192KSKCM1
p.L184IREAD1
p.S196FLIHC1
p.S206FSKCM1
p.W171RPRAD1
p.G64ESKCM1
p.R181QSKCM1
p.G227RSTAD1
p.Q146EPRAD1
p.V213MSTAD1
p.R181QKICH1
p.T134ILGG1
p.R126HSTAD1
p.W229RLIHC1
p.Y177CLUAD1
p.L197FBRCA1
p.R128QSKCM1
p.Y177CPRAD1


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TissGeneCNV for NKX3-1

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 NKX3-1

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
Chimerdb3.0ChiTaRsNABI855676NKX3-1-SNRPD1chr8:23536680chr18:19209074


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TissGeneNet for NKX3-1

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)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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COAD (tumor)COAD (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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HNSC (tumor)HNSC (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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KICH (tumor)KICH (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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KIRC (tumor)KIRC (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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KIRP (tumor)KIRP (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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LIHC (tumor)LIHC (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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LUAD (tumor)LUAD (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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LUSC (tumor)LUSC (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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PRAD (tumor)PRAD (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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STAD (tumor)STAD (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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THCA (tumor)THCA (normal)
NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (tumor)NKX3-1, HIPK2, SP1, HDAC1, KAT2B, SP4, SP3, SRF, TOPORS, TOP1, SP2, SP5, SPDEF (normal)
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TissGeneProg for NKX3-1

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 NKX3-1
TissGeneDrug for NKX3-1

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 NKX3-1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0376358Malignant neoplasm of prostate62BeFree,GAD,MGD
umls:C0600139Prostate carcinoma58BeFree
umls:C0033578Prostatic Neoplasms25BeFree,CTD_human,LHGDN
umls:C0596263Carcinogenesis16BeFree
umls:C1654637androgen independent prostate cancer4BeFree
umls:C0027627Neoplasm Metastasis3BeFree
umls:C0178874Tumor Progression3BeFree
umls:C0282612Prostatic Intraepithelial Neoplasias3BeFree
umls:C0936223Metastatic Prostate Carcinoma3BeFree
umls:C0001418Adenocarcinoma2BeFree
umls:C0027658Neoplasms, Germ Cell and Embryonal2LHGDN
umls:C0598935Tumor Initiation2BeFree
umls:C0686619Secondary malignant neoplasm of lymph node2BeFree
umls:C1168327High-Grade Prostatic Intraepithelial Neoplasia2BeFree
umls:C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma2BeFree
umls:C2931456Prostate cancer, familial2BeFree
umls:C2937421Prostatic Hyperplasia2BeFree,GAD
umls:C0002793Anaplasia1BeFree
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0007112Adenocarcinoma of prostate1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0014599Epithelial hyperplasia1BeFree
umls:C0023418leukemia1BeFree
umls:C0023448Lymphoid leukemia1BeFree
umls:C0023449Acute lymphocytic leukemia1BeFree
umls:C0036631Seminoma1BeFree
umls:C0151514Atrophic condition of skin1BeFree
umls:C0153594Malignant neoplasm of testis1BeFree
umls:C0205851Germ cell tumor1BeFree
umls:C0206659Embryonal Carcinoma1BeFree
umls:C0206692Carcinoma, Lobular1LHGDN
umls:C0278838Prostate cancer recurrent1BeFree
umls:C0677898invasive cancer1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C0855197Testicular malignant germ cell tumor1BeFree
umls:C0878500Intraepithelial Neoplasia1BeFree
umls:C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1BeFree