TissGeneSummary for NR1H4 |
Gene summary |
Basic gene information | Gene symbol | NR1H4 |
Gene name | nuclear receptor subfamily 1, group H, member 4 | |
Synonyms | BAR|FXR|HRR-1|HRR1|RIP14 | |
Cytomap | UCSC genome browser: 12q23.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001206977.1, NM_001206978.1,NM_001206979.1,NM_001206992.1,NM_001206993.1, NM_005123.3, | |
Description | RXR-interacting protein 14bile acid receptorfarnesoid X nuclear receptorfarnesoid X-activated receptorfarnesol receptor HRR-1retinoid X receptor-interacting protein 14 | |
Modification date | 20141207 | |
dbXrefs | MIM : 603826 | |
HGNC : HGNC | ||
Ensembl : ENSG00000012504 | ||
HPRD : 04827 | ||
Vega : OTTHUMG00000170359 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NR1H4 | |
BioGPS: 9971 | ||
Pathway | NCI Pathway Interaction Database: NR1H4 | |
KEGG: NR1H4 | ||
REACTOME: NR1H4 | ||
Pathway Commons: NR1H4 | ||
Context | iHOP: NR1H4 | |
ligand binding site mutation search in PubMed: NR1H4 | ||
UCL Cancer Institute: NR1H4 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,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. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID | GO:0038185 | intracellular bile acid receptor signaling pathway | 10334992 | GO:0070858 | negative regulation of bile acid biosynthetic process | 10334992 | GO:0038185 | intracellular bile acid receptor signaling pathway | 10334992 | GO:0070858 | negative regulation of bile acid biosynthetic process | 10334992 |
Top |
TissGeneExp for NR1H4 |
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 |
COAD | 0.280756115 | 4.697506115 | -4.41675 | 4.36E-10 | 5.22E-09 |
LUSC | -1.719413266 | -0.027605423 | -1.691807843 | 4.38E-12 | 1.91E-11 |
KICH | -0.138929423 | 6.796890577 | -6.93582 | 7.43E-15 | 1.46E-13 |
BLCA | -0.216552792 | 2.259947208 | -2.4765 | 0.00256 | 0.015555847 |
PRAD | -1.091824654 | 0.043000346 | -1.134825 | 2.65E-05 | 0.00013052 |
Top |
TissGene-miRNA for NR1H4 |
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 |
Top |
TissGeneMut for NR1H4 |
TissGeneSNV for NR1H4 |
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.S62F | SKCM | 2 |
p.T219I | SKCM | 1 |
p.S72F | SKCM | 1 |
p.R113S | HNSC | 1 |
p.D312N | SKCM | 1 |
p.A333V | SKCM | 1 |
p.M452I | KIRC | 1 |
p.L412F | LUAD | 1 |
p.P477T | LUSC | 1 |
p.P306T | PAAD | 1 |
p.R227C | SKCM | 1 |
p.Q6* | LUSC | 1 |
p.R363Q | READ | 1 |
p.R176* | SARC | 1 |
p.A35T | GBM | 1 |
p.N271S | COAD | 1 |
p.R363X | COAD | 1 |
p.R153T | LUAD | 1 |
p.P11L | SKCM | 1 |
p.R186Q | SKCM | 1 |
p.P77S | SKCM | 1 |
p.A159S | LUAD | 1 |
p.N178S | SKCM | 1 |
p.I286M | UCEC | 1 |
p.E87K | SKCM | 1 |
p.R153I | UCEC | 1 |
p.T288M | OV | 1 |
p.R163T | LUAD | 1 |
p.P22L | LUAD | 1 |
p.S205P | HNSC | 1 |
p.R153S | LUAD | 1 |
p.G226D | SKCM | 1 |
p.R123C | CESC | 1 |
p.Q39H | LUAD | 1 |
p.I12N | OV | 1 |
p.E100K | SKCM | 1 |
p.A128S | THYM | 1 |
p.E314D | STAD | 1 |
p.H10N | LUSC | 1 |
p.P320T | PAAD | 1 |
p.R331C | UCS | 1 |
p.S219P | HNSC | 1 |
p.R100H | COAD | 1 |
p.M30I | GBM | 1 |
p.R331H | UCEC | 1 |
p.M200I | LUAD | 1 |
p.E374* | HNSC | 1 |
p.D134E | LUSC | 1 |
p.D484N | LIHC | 1 |
p.R176Q | SKCM | 1 |
p.S64L | LUAD | 1 |
p.R90H | STAD | 1 |
p.P107L | SKCM | 1 |
p.R331C | SKCM | 1 |
p.E360* | HNSC | 1 |
p.Q232L | LUSC | 1 |
p.N168S | SKCM | 1 |
p.V428A | STAD | 1 |
p.F284V | UCEC | 1 |
p.A343V | SKCM | 1 |
p.T257S | KIRC | 1 |
p.L197V | UCS | 1 |
p.T143I | LUAD | 1 |
p.E110K | SKCM | 1 |
p.V389F | ESCA | 1 |
p.R187I | COAD | 1 |
p.T243S | KIRC | 1 |
p.L218P | SKCM | 1 |
p.N235S | UCEC | 1 |
p.D322N | SKCM | 1 |
p.R100H | STAD | 1 |
p.G84R | SKCM | 1 |
p.E205X | ESCA | 1 |
p.L208P | SKCM | 1 |
p.R353Q | SKCM | 1 |
p.P55S | BLCA | 1 |
p.Y81* | BLCA | 1 |
p.R100H | GBM | 1 |
p.D268E | COAD | 1 |
p.S82C | BLCA | 1 |
p.Y397H | BLCA | 1 |
p.E28V | LUAD | 1 |
p.S31R | LUSC | 1 |
p.L426F | LUAD | 1 |
p.D17Y | UCEC | 1 |
p.E282X | PAAD | 1 |
p.A324G | LUAD | 1 |
p.L211V | UCS | 1 |
p.E349K | LGG | 1 |
p.R345C | UCS | 1 |
p.R123S | HNSC | 1 |
p.T229I | SKCM | 1 |
p.P87S | SKCM | 1 |
p.R341C | SKCM | 1 |
p.D217H | BRCA | 1 |
p.Y96F | STAD | 1 |
p.S238L | SKCM | 1 |
p.Q393K | LIHC | 1 |
p.Y208S | LIHC | 1 |
p.R113C | CESC | 1 |
p.E205K | LUAD | 1 |
p.L412I | UCEC | 1 |
p.M1K | COAD | 1 |
p.S248L | SKCM | 1 |
p.G131* | UCEC | 1 |
p.A383V | HNSC | 1 |
p.E296Q | LUSC | 1 |
p.C20F | LUAD | 1 |
p.E28K | SKCM | 1 |
p.P65T | COAD | 1 |
p.L208P | LUAD | 1 |
Top |
TissGeneCNV for NR1H4 |
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) |
Top |
TissGeneFusions for NR1H4 |
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 |
Top |
TissGeneNet for NR1H4 |
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) |
Top |
TissGeneProg for NR1H4 |
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. |
Top |
TissGeneClin for NR1H4 |
TissGeneDrug for NR1H4 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
DB05990 | Obeticholic acid | Agonist | Small molecule | Approved |
DB06777 | Chenodeoxycholic acid | Other | Small molecule | Approved |
Top |
TissGeneDisease for NR1H4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0008370 | Cholestasis | 10 | BeFree,CTD_human,LHGDN |
umls:C0023903 | Liver neoplasms | 6 | BeFree,CTD_human |
umls:C2239176 | Liver carcinoma | 6 | BeFree,CTD_human,MGD |
umls:C0023895 | Liver diseases | 5 | BeFree,CTD_human,LHGDN |
umls:C0008350 | Cholelithiasis | 3 | BeFree,GAD |
umls:C0008372 | Intrahepatic Cholestasis | 3 | GAD,LHGDN,RGD |
umls:C0010068 | Coronary heart disease | 3 | BeFree,GAD |
umls:C0010346 | Crohn Disease | 3 | BeFree,CTD_human |
umls:C0028754 | Obesity | 3 | BeFree |
umls:C0011847 | Diabetes | 2 | BeFree |
umls:C0011849 | Diabetes Mellitus | 2 | BeFree |
umls:C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 2 | BeFree |
umls:C0016667 | Fragile X Syndrome | 2 | BeFree |
umls:C0019163 | Hepatitis B | 2 | BeFree |
umls:C0020538 | Hypertensive disease | 2 | BeFree |
umls:C0021390 | Inflammatory Bowel Diseases | 2 | BeFree |
umls:C0268312 | Progressive intrahepatic cholestasis (disorder) | 2 | BeFree |
umls:C0268318 | Cholestasis of pregnancy | 2 | BeFree,ORPHANET |
umls:C0279628 | Adenocarcinoma Of Esophagus | 2 | BeFree |
umls:C0596263 | Carcinogenesis | 2 | BeFree |
umls:C0856727 | Cholesterol gallstones | 2 | BeFree |
umls:C0860204 | Cholestatic liver disease | 2 | BeFree |
umls:C0947622 | Cholecystolithiasis | 2 | BeFree,GAD |
umls:C0001339 | Acute pancreatitis | 1 | BeFree |
umls:C0001418 | Adenocarcinoma | 1 | LHGDN |
umls:C0002395 | Alzheimer's Disease | 1 | GAD |
umls:C0004153 | Atherosclerosis | 1 | GAD |
umls:C0004763 | Barrett Esophagus | 1 | LHGDN |
umls:C0005398 | Cholestasis, Extrahepatic | 1 | RGD |
umls:C0005684 | Malignant neoplasm of urinary bladder | 1 | GAD |
umls:C0007113 | Rectal Carcinoma | 1 | BeFree |
umls:C0007137 | Squamous cell carcinoma | 1 | BeFree |
umls:C0009319 | Colitis | 1 | BeFree |
umls:C0009324 | Ulcerative Colitis | 1 | BeFree |
umls:C0011853 | Diabetes Mellitus, Experimental | 1 | RGD |
umls:C0014868 | Esophagitis | 1 | LHGDN |
umls:C0015379 | Extravasation of Diagnostic and Therapeutic Materials | 1 | CTD_human |
umls:C0015695 | Fatty Liver | 1 | LHGDN |
umls:C0019693 | HIV Infections | 1 | BeFree |
umls:C0020473 | Hyperlipidemia | 1 | BeFree |
umls:C0021368 | Inflammation | 1 | GAD |
umls:C0021655 | Insulin Resistance | 1 | GAD |
umls:C0021841 | Intestinal Neoplasms | 1 | CTD_human |
umls:C0023434 | Chronic Lymphocytic Leukemia | 1 | BeFree |
umls:C0023890 | Liver Cirrhosis | 1 | GAD |
umls:C0024117 | Chronic Obstructive Airway Disease | 1 | GAD |
umls:C0025517 | Metabolic Diseases | 1 | BeFree |
umls:C0026266 | Mitral Valve Insufficiency | 1 | BeFree |
umls:C0027627 | Neoplasm Metastasis | 1 | BeFree |
umls:C0028756 | Obesity, Morbid | 1 | BeFree |
umls:C0032584 | polyps | 1 | BeFree |
umls:C0032962 | Pregnancy Complications | 1 | GAD |
umls:C0038454 | Cerebrovascular accident | 1 | BeFree |
umls:C0042769 | Virus Diseases | 1 | BeFree |
umls:C0235974 | Pancreatic carcinoma | 1 | BeFree |
umls:C0238052 | Xanthomatosis, Cerebrotendinous | 1 | BeFree,LHGDN |
umls:C0239946 | Fibrosis, Liver | 1 | BeFree |
umls:C0242379 | Malignant neoplasm of lung | 1 | GAD |
umls:C0266470 | Cerebellar Hypoplasia | 1 | BeFree |
umls:C0279000 | Liver and Intrahepatic Biliary Tract Carcinoma | 1 | BeFree |
umls:C0345904 | Malignant neoplasm of liver | 1 | BeFree |
umls:C0346647 | Malignant neoplasm of pancreas | 1 | BeFree |
umls:C0524851 | Neurodegenerative Disorders | 1 | BeFree |
umls:C0559031 | Functional Gastrointestinal Disorders | 1 | BeFree |
umls:C0566602 | Primary sclerosing cholangitis | 1 | BeFree |
umls:C0600452 | Hepatopulmonary Syndrome | 1 | GAD |
umls:C0860207 | Drug-Induced Liver Injury | 1 | CTD_human |
umls:C0870082 | Hyperkeratosis | 1 | BeFree |
umls:C0948008 | Ischemic stroke | 1 | BeFree |
umls:C1176475 | Ductal Carcinoma | 1 | LHGDN |
umls:C1290884 | Inflammatory disorder | 1 | BeFree |
umls:C1458155 | Mammary Neoplasms | 1 | LHGDN |
umls:C3241937 | Nonalcoholic Steatohepatitis | 1 | BeFree |
umls:C3272363 | Ischemic Cerebrovascular Accident | 1 | BeFree |
umls:C3714514 | Infection | 1 | LHGDN |