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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 NR1H4
check button Gene summary
Basic gene informationGene symbolNR1H4
Gene namenuclear receptor subfamily 1, group H, member 4
SynonymsBAR|FXR|HRR-1|HRR1|RIP14
CytomapUCSC genome browser: 12q23.1
Type of geneprotein-coding
RefGenesNM_001206977.1,
NM_001206978.1,NM_001206979.1,NM_001206992.1,NM_001206993.1,
NM_005123.3,
DescriptionRXR-interacting protein 14bile acid receptorfarnesoid X nuclear receptorfarnesoid X-activated receptorfarnesol receptor HRR-1retinoid X receptor-interacting protein 14
Modification date20141207
dbXrefs MIM : 603826
HGNC : HGNC
Ensembl : ENSG00000012504
HPRD : 04827
Vega : OTTHUMG00000170359
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NR1H4
BioGPS: 9971
PathwayNCI Pathway Interaction Database: NR1H4
KEGG: NR1H4
REACTOME: NR1H4
Pathway Commons: NR1H4
ContextiHOP: NR1H4
ligand binding site mutation search in PubMed: NR1H4
UCL Cancer Institute: NR1H4
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)KidneyLiver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)KIRC,KIRP,KICHLIHC
Reference showing the relevant tissue of NR1H4
Description by TissGene annotations
* 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:0038185intracellular bile acid receptor signaling pathway10334992
GO:0070858negative regulation of bile acid biosynthetic process10334992
GO:0038185intracellular bile acid receptor signaling pathway10334992
GO:0070858negative regulation of bile acid biosynthetic process10334992


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TissGeneExp for NR1H4

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
COAD0.2807561154.697506115-4.416754.36E-105.22E-09
LUSC-1.719413266-0.027605423-1.6918078434.38E-121.91E-11
KICH-0.1389294236.796890577-6.935827.43E-151.46E-13
BLCA-0.2165527922.259947208-2.47650.002560.015555847
PRAD-1.0918246540.043000346-1.1348252.65E-050.00013052


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TissGene-miRNA for NR1H4

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 NR1H4
TissGeneSNV for NR1H4

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.S62FSKCM2
p.T219ISKCM1
p.S72FSKCM1
p.R113SHNSC1
p.D312NSKCM1
p.A333VSKCM1
p.M452IKIRC1
p.L412FLUAD1
p.P477TLUSC1
p.P306TPAAD1
p.R227CSKCM1
p.Q6*LUSC1
p.R363QREAD1
p.R176*SARC1
p.A35TGBM1
p.N271SCOAD1
p.R363XCOAD1
p.R153TLUAD1
p.P11LSKCM1
p.R186QSKCM1
p.P77SSKCM1
p.A159SLUAD1
p.N178SSKCM1
p.I286MUCEC1
p.E87KSKCM1
p.R153IUCEC1
p.T288MOV1
p.R163TLUAD1
p.P22LLUAD1
p.S205PHNSC1
p.R153SLUAD1
p.G226DSKCM1
p.R123CCESC1
p.Q39HLUAD1
p.I12NOV1
p.E100KSKCM1
p.A128STHYM1
p.E314DSTAD1
p.H10NLUSC1
p.P320TPAAD1
p.R331CUCS1
p.S219PHNSC1
p.R100HCOAD1
p.M30IGBM1
p.R331HUCEC1
p.M200ILUAD1
p.E374*HNSC1
p.D134ELUSC1
p.D484NLIHC1
p.R176QSKCM1
p.S64LLUAD1
p.R90HSTAD1
p.P107LSKCM1
p.R331CSKCM1
p.E360*HNSC1
p.Q232LLUSC1
p.N168SSKCM1
p.V428ASTAD1
p.F284VUCEC1
p.A343VSKCM1
p.T257SKIRC1
p.L197VUCS1
p.T143ILUAD1
p.E110KSKCM1
p.V389FESCA1
p.R187ICOAD1
p.T243SKIRC1
p.L218PSKCM1
p.N235SUCEC1
p.D322NSKCM1
p.R100HSTAD1
p.G84RSKCM1
p.E205XESCA1
p.L208PSKCM1
p.R353QSKCM1
p.P55SBLCA1
p.Y81*BLCA1
p.R100HGBM1
p.D268ECOAD1
p.S82CBLCA1
p.Y397HBLCA1
p.E28VLUAD1
p.S31RLUSC1
p.L426FLUAD1
p.D17YUCEC1
p.E282XPAAD1
p.A324GLUAD1
p.L211VUCS1
p.E349KLGG1
p.R345CUCS1
p.R123SHNSC1
p.T229ISKCM1
p.P87SSKCM1
p.R341CSKCM1
p.D217HBRCA1
p.Y96FSTAD1
p.S238LSKCM1
p.Q393KLIHC1
p.Y208SLIHC1
p.R113CCESC1
p.E205KLUAD1
p.L412IUCEC1
p.M1KCOAD1
p.S248LSKCM1
p.G131*UCEC1
p.A383VHNSC1
p.E296QLUSC1
p.C20FLUAD1
p.E28KSKCM1
p.P65TCOAD1
p.L208PLUAD1


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TissGeneCNV for NR1H4

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 NR1H4

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


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TissGeneNet for NR1H4

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)
NR1H4, RELA, SRC, NR0B2, ESR1, RXRA, HIST1H3A, NCOA1, EP300, SIRT1, KRT17, PPARA, PRMT1, APOA1, PRKCZ, PPARGC1A, PRKDC, SLC2A4, APOA5, FGF19, FABP6 (tumor)NR1H4, XRCC5, NCOR1, SRC, NR0B2, ESR1, HIST1H3A, GAPDH, HIST1H4A, EP300, SIRT1, CARM1, PPARA, PRMT1, APOA1, PPARGC1A, PRKDC, APOA5, BAAT, FABP6, SLCO1B3 (normal)
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COAD (tumor)COAD (normal)
NR1H4, SRC, ESR1, RXRA, NCOA1, RXRG, SMARCD1, HNF1A, CARM1, PPARA, PRMT1, APOA1, PRKCZ, PPARGC1A, SMARCD3, GPS2, APOA5, SLC27A5, FGF19, BAAT, FABP6 (tumor)NR1H4, XRCC5, CASP8, NCOR1, RELA, RXRA, GAPDH, RXRG, EP300, NCOA6, HNF1A, CARM1, PPARA, APOA1, PRKCZ, PPARGC1A, SMARCD3, PRKDC, GPS2, SLC27A5, BAAT (normal)
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HNSC (tumor)HNSC (normal)
NR1H4, XRCC5, GRB2, RELA, SRC, NR0B2, ESR1, RXRA, HIST1H3A, RXRG, NCOA6, SMARCD1, PPARA, PRMT1, APOA1, PRKCZ, PPARGC1A, SMARCD3, SLC2A4, FGF19, SLCO1B3 (tumor)NR1H4, XRCC5, CASP8, RELA, SRC, NR0B2, ESR1, RXRA, NCOR2, EP300, NCOA6, KRT17, HNF1A, CARM1, APOA1, SMARCD3, SLC2A4, APOA5, SLC27A5, BAAT, SLCO1B3 (normal)
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KICH (tumor)KICH (normal)
NR1H4, NCOR1, SRC, HIST1H3A, GAPDH, NCOA1, HIST1H4A, NCOR2, EP300, NCOA6, HNF1A, CARM1, PRMT1, APOA1, PRKDC, XRCC6, SLC2A4, RRM2, APOA5, SLC27A5, BAAT (tumor)NR1H4, XRCC5, CASP8, GRB2, NCOR1, RELA, HIST1H3A, GAPDH, NCOA1, RXRG, NCOR2, SIRT1, HNF1A, CARM1, PRMT1, APOA1, PPARGC1A, XRCC6, SLC2A4, GPS2, APOA5 (normal)
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KIRC (tumor)KIRC (normal)
NR1H4, CASP8, GRB2, NCOR1, RELA, SRC, NR0B2, ESR1, GAPDH, NCOA1, NCOR2, SIRT1, HNF1A, CARM1, PPARGC1A, SMARCD3, PRKDC, SLC2A4, RRM2, BAAT, FABP6 (tumor)NR1H4, CASP8, GRB2, NR0B2, ESR1, GAPDH, SIRT1, KRT17, HNF1A, CARM1, PRMT1, PRKCZ, SMARCD3, XRCC6, SLC2A4, RRM2, SLC27A5, FGF19, BAAT, FABP6, SLCO1B3 (normal)
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KIRP (tumor)KIRP (normal)
NR1H4, XRCC5, CASP8, SRC, NR0B2, ESR1, GAPDH, NCOR2, EP300, SIRT1, SMARCD1, HNF1A, CARM1, PRMT1, SMARCD3, SLC2A4, RRM2, GPS2, BAAT, FABP6, SLCO1B3 (tumor)NR1H4, GRB2, RELA, SRC, RXRA, NCOA1, RXRG, EP300, KRT17, SMARCD1, HNF1A, CARM1, PPARA, PRMT1, PRKCZ, PPARGC1A, XRCC6, RRM2, APOA5, FABP6, SLCO1B3 (normal)
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LIHC (tumor)LIHC (normal)
NR1H4, CASP8, GRB2, NCOR1, RELA, SRC, NCOA1, HIST1H4A, NCOR2, EP300, SIRT1, SMARCD1, PPARA, PRMT1, PRKCZ, SMARCD3, RRM2, FGF19, BAAT, FABP6, SLCO1B3 (tumor)NR1H4, NR0B2, ESR1, RXRA, GAPDH, NCOR2, KRT17, SMARCD1, HNF1A, CARM1, PPARA, PRMT1, APOA1, PRKCZ, PPARGC1A, SMARCD3, SLC2A4, RRM2, APOA5, SLC27A5, BAAT (normal)
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LUAD (tumor)LUAD (normal)
NR1H4, CASP8, HIST1H4A, RXRG, NCOR2, SIRT1, NCOA6, KRT17, SMARCD1, CARM1, APOA1, PRKCZ, SMARCD3, PRKDC, SLC2A4, RRM2, GPS2, APOA5, SLC27A5, BAAT, SLCO1B3 (tumor)NR1H4, XRCC5, GRB2, SRC, NR0B2, EP300, NCOA6, KRT17, HNF1A, CARM1, PPARA, APOA1, PRKCZ, PPARGC1A, PRKDC, XRCC6, GPS2, APOA5, FGF19, BAAT, SLCO1B3 (normal)
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LUSC (tumor)LUSC (normal)
NR1H4, CASP8, RELA, SRC, NR0B2, ESR1, HIST1H3A, GAPDH, RXRG, NCOR2, EP300, SIRT1, NCOA6, KRT17, CARM1, PPARA, PRKDC, SLC2A4, GPS2, SLC27A5, FGF19 (tumor)NR1H4, NR0B2, ESR1, RXRA, GAPDH, RXRG, SIRT1, KRT17, HNF1A, CARM1, PPARA, APOA1, PRKCZ, PPARGC1A, SMARCD3, PRKDC, XRCC6, SLC2A4, GPS2, APOA5, BAAT (normal)
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PRAD (tumor)PRAD (normal)
NR1H4, XRCC5, GRB2, RELA, SRC, GAPDH, NCOA1, SIRT1, SMARCD1, PPARA, APOA1, PRKCZ, PPARGC1A, SMARCD3, XRCC6, SLC2A4, RRM2, GPS2, APOA5, SLC27A5, FGF19 (tumor)NR1H4, XRCC5, CASP8, GRB2, NCOR1, RELA, SRC, RXRA, NCOA1, RXRG, NCOR2, HNF1A, PPARA, APOA1, PPARGC1A, SMARCD3, XRCC6, APOA5, FGF19, BAAT, FABP6 (normal)
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STAD (tumor)STAD (normal)
NR1H4, XRCC5, CASP8, GRB2, NCOR1, RELA, SRC, NR0B2, HIST1H4A, SIRT1, HNF1A, PPARA, APOA1, PRKCZ, PRKDC, XRCC6, SLC2A4, GPS2, APOA5, BAAT, FABP6 (tumor)NR1H4, RELA, SRC, NR0B2, GAPDH, NCOA1, HIST1H4A, RXRG, NCOA6, SMARCD1, HNF1A, CARM1, PPARA, APOA1, PRKCZ, SMARCD3, APOA5, SLC27A5, FGF19, BAAT, FABP6 (normal)
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THCA (tumor)THCA (normal)
NR1H4, XRCC5, CASP8, GRB2, NCOR1, SRC, NR0B2, RXRA, NCOA1, SMARCD1, HNF1A, APOA1, PRKCZ, PPARGC1A, SMARCD3, PRKDC, XRCC6, RRM2, SLC27A5, BAAT, FABP6 (tumor)NR1H4, CASP8, GRB2, NCOR1, NR0B2, RXRA, HIST1H3A, NCOA1, RXRG, NCOR2, NCOA6, SMARCD1, HNF1A, APOA1, PRKCZ, PPARGC1A, SMARCD3, APOA5, SLC27A5, BAAT, SLCO1B3 (normal)
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TissGeneProg for NR1H4

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 NR1H4
TissGeneDrug for NR1H4

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB05990Obeticholic acidAgonistSmall moleculeApproved
DB06777Chenodeoxycholic acidOtherSmall moleculeApproved


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TissGeneDisease for NR1H4

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0008370Cholestasis10BeFree,CTD_human,LHGDN
umls:C0023903Liver neoplasms6BeFree,CTD_human
umls:C2239176Liver carcinoma6BeFree,CTD_human,MGD
umls:C0023895Liver diseases5BeFree,CTD_human,LHGDN
umls:C0008350Cholelithiasis3BeFree,GAD
umls:C0008372Intrahepatic Cholestasis3GAD,LHGDN,RGD
umls:C0010068Coronary heart disease3BeFree,GAD
umls:C0010346Crohn Disease3BeFree,CTD_human
umls:C0028754Obesity3BeFree
umls:C0011847Diabetes2BeFree
umls:C0011849Diabetes Mellitus2BeFree
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent2BeFree
umls:C0016667Fragile X Syndrome2BeFree
umls:C0019163Hepatitis B2BeFree
umls:C0020538Hypertensive disease2BeFree
umls:C0021390Inflammatory Bowel Diseases2BeFree
umls:C0268312Progressive intrahepatic cholestasis (disorder)2BeFree
umls:C0268318Cholestasis of pregnancy2BeFree,ORPHANET
umls:C0279628Adenocarcinoma Of Esophagus2BeFree
umls:C0596263Carcinogenesis2BeFree
umls:C0856727Cholesterol gallstones2BeFree
umls:C0860204Cholestatic liver disease2BeFree
umls:C0947622Cholecystolithiasis2BeFree,GAD
umls:C0001339Acute pancreatitis1BeFree
umls:C0001418Adenocarcinoma1LHGDN
umls:C0002395Alzheimer's Disease1GAD
umls:C0004153Atherosclerosis1GAD
umls:C0004763Barrett Esophagus1LHGDN
umls:C0005398Cholestasis, Extrahepatic1RGD
umls:C0005684Malignant neoplasm of urinary bladder1GAD
umls:C0007113Rectal Carcinoma1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0009319Colitis1BeFree
umls:C0009324Ulcerative Colitis1BeFree
umls:C0011853Diabetes Mellitus, Experimental1RGD
umls:C0014868Esophagitis1LHGDN
umls:C0015379Extravasation of Diagnostic and Therapeutic Materials1CTD_human
umls:C0015695Fatty Liver1LHGDN
umls:C0019693HIV Infections1BeFree
umls:C0020473Hyperlipidemia1BeFree
umls:C0021368Inflammation1GAD
umls:C0021655Insulin Resistance1GAD
umls:C0021841Intestinal Neoplasms1CTD_human
umls:C0023434Chronic Lymphocytic Leukemia1BeFree
umls:C0023890Liver Cirrhosis1GAD
umls:C0024117Chronic Obstructive Airway Disease1GAD
umls:C0025517Metabolic Diseases1BeFree
umls:C0026266Mitral Valve Insufficiency1BeFree
umls:C0027627Neoplasm Metastasis1BeFree
umls:C0028756Obesity, Morbid1BeFree
umls:C0032584polyps1BeFree
umls:C0032962Pregnancy Complications1GAD
umls:C0038454Cerebrovascular accident1BeFree
umls:C0042769Virus Diseases1BeFree
umls:C0235974Pancreatic carcinoma1BeFree
umls:C0238052Xanthomatosis, Cerebrotendinous1BeFree,LHGDN
umls:C0239946Fibrosis, Liver1BeFree
umls:C0242379Malignant neoplasm of lung1GAD
umls:C0266470Cerebellar Hypoplasia1BeFree
umls:C0279000Liver and Intrahepatic Biliary Tract Carcinoma1BeFree
umls:C0345904Malignant neoplasm of liver1BeFree
umls:C0346647Malignant neoplasm of pancreas1BeFree
umls:C0524851Neurodegenerative Disorders1BeFree
umls:C0559031Functional Gastrointestinal Disorders1BeFree
umls:C0566602Primary sclerosing cholangitis1BeFree
umls:C0600452Hepatopulmonary Syndrome1GAD
umls:C0860207Drug-Induced Liver Injury1CTD_human
umls:C0870082Hyperkeratosis1BeFree
umls:C0948008Ischemic stroke1BeFree
umls:C1176475Ductal Carcinoma1LHGDN
umls:C1290884Inflammatory disorder1BeFree
umls:C1458155Mammary Neoplasms1LHGDN
umls:C3241937Nonalcoholic Steatohepatitis1BeFree
umls:C3272363Ischemic Cerebrovascular Accident1BeFree
umls:C3714514Infection1LHGDN