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Gene: NR1H4 |
Gene summary for NR1H4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NR1H4 | Gene ID | 9971 |
| Gene name | nuclear receptor subfamily 1 group H member 4 | |
| Gene Alias | BAR | |
| Cytomap | 12q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | F1DAL1 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 9971 | NR1H4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.01e-04 | -2.52e-01 | 0.294 |
| 9971 | NR1H4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.10e-08 | -2.77e-01 | 0.3859 |
| 9971 | NR1H4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.40e-10 | -2.87e-01 | 0.3005 |
| 9971 | NR1H4 | A002-C-010 | Human | Colorectum | FAP | 1.48e-08 | -2.74e-01 | 0.242 |
| 9971 | NR1H4 | A015-C-203 | Human | Colorectum | FAP | 1.64e-09 | -2.69e-01 | -0.1294 |
| 9971 | NR1H4 | A002-C-201 | Human | Colorectum | FAP | 2.00e-04 | -2.51e-01 | 0.0324 |
| 9971 | NR1H4 | A002-C-203 | Human | Colorectum | FAP | 7.75e-08 | -2.32e-01 | 0.2786 |
| 9971 | NR1H4 | A001-C-119 | Human | Colorectum | FAP | 5.95e-03 | -2.70e-01 | -0.1557 |
| 9971 | NR1H4 | A001-C-108 | Human | Colorectum | FAP | 4.33e-08 | -2.50e-01 | -0.0272 |
| 9971 | NR1H4 | A002-C-021 | Human | Colorectum | FAP | 1.95e-11 | -2.88e-01 | 0.1171 |
| 9971 | NR1H4 | A002-C-205 | Human | Colorectum | FAP | 9.67e-07 | -2.85e-01 | -0.1236 |
| 9971 | NR1H4 | A001-C-104 | Human | Colorectum | FAP | 2.74e-04 | -2.36e-01 | 0.0184 |
| 9971 | NR1H4 | A015-C-005 | Human | Colorectum | FAP | 8.48e-03 | -2.60e-01 | -0.0336 |
| 9971 | NR1H4 | A015-C-006 | Human | Colorectum | FAP | 1.57e-05 | -2.96e-01 | -0.0994 |
| 9971 | NR1H4 | A015-C-106 | Human | Colorectum | FAP | 1.27e-10 | -2.67e-01 | -0.0511 |
| 9971 | NR1H4 | A002-C-114 | Human | Colorectum | FAP | 2.69e-07 | -2.96e-01 | -0.1561 |
| 9971 | NR1H4 | A015-C-104 | Human | Colorectum | FAP | 1.58e-13 | -2.84e-01 | -0.1899 |
| 9971 | NR1H4 | A001-C-014 | Human | Colorectum | FAP | 9.34e-11 | -2.89e-01 | 0.0135 |
| 9971 | NR1H4 | A002-C-016 | Human | Colorectum | FAP | 1.06e-07 | -2.57e-01 | 0.0521 |
| 9971 | NR1H4 | A015-C-002 | Human | Colorectum | FAP | 2.85e-04 | -2.96e-01 | -0.0763 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000974912 | Liver | HCC | response to glucose | 121/7958 | 212/18723 | 1.24e-05 | 1.39e-04 | 121 |
| GO:007139821 | Liver | HCC | cellular response to fatty acid | 29/7958 | 38/18723 | 2.35e-05 | 2.47e-04 | 29 |
| GO:004312212 | Liver | HCC | regulation of I-kappaB kinase/NF-kappaB signaling | 138/7958 | 249/18723 | 2.47e-05 | 2.58e-04 | 138 |
| GO:00082062 | Liver | HCC | bile acid metabolic process | 34/7958 | 49/18723 | 1.28e-04 | 1.06e-03 | 34 |
| GO:19016172 | Liver | HCC | organic hydroxy compound biosynthetic process | 129/7958 | 237/18723 | 1.32e-04 | 1.08e-03 | 129 |
| GO:00468902 | Liver | HCC | regulation of lipid biosynthetic process | 96/7958 | 171/18723 | 2.14e-04 | 1.63e-03 | 96 |
| GO:00105652 | Liver | HCC | regulation of cellular ketone metabolic process | 77/7958 | 133/18723 | 2.41e-04 | 1.80e-03 | 77 |
| GO:00066992 | Liver | HCC | bile acid biosynthetic process | 26/7958 | 36/18723 | 2.93e-04 | 2.10e-03 | 26 |
| GO:004259322 | Liver | HCC | glucose homeostasis | 137/7958 | 258/18723 | 3.59e-04 | 2.49e-03 | 137 |
| GO:003350022 | Liver | HCC | carbohydrate homeostasis | 137/7958 | 259/18723 | 4.45e-04 | 2.98e-03 | 137 |
| GO:000167822 | Liver | HCC | cellular glucose homeostasis | 95/7958 | 172/18723 | 4.95e-04 | 3.24e-03 | 95 |
| GO:007133112 | Liver | HCC | cellular response to hexose stimulus | 85/7958 | 153/18723 | 7.47e-04 | 4.52e-03 | 85 |
| GO:007133312 | Liver | HCC | cellular response to glucose stimulus | 84/7958 | 151/18723 | 7.57e-04 | 4.56e-03 | 84 |
| GO:007132612 | Liver | HCC | cellular response to monosaccharide stimulus | 85/7958 | 154/18723 | 9.78e-04 | 5.68e-03 | 85 |
| GO:0038183 | Liver | HCC | bile acid signaling pathway | 12/7958 | 14/18723 | 1.17e-03 | 6.54e-03 | 12 |
| GO:0009064 | Liver | HCC | glutamine family amino acid metabolic process | 47/7958 | 78/18723 | 1.17e-03 | 6.54e-03 | 47 |
| GO:007132212 | Liver | HCC | cellular response to carbohydrate stimulus | 89/7958 | 163/18723 | 1.19e-03 | 6.62e-03 | 89 |
| GO:0006654 | Liver | HCC | phosphatidic acid biosynthetic process | 23/7958 | 33/18723 | 1.46e-03 | 7.75e-03 | 23 |
| GO:0002224 | Liver | HCC | toll-like receptor signaling pathway | 67/7958 | 121/18723 | 2.87e-03 | 1.34e-02 | 67 |
| GO:00550902 | Liver | HCC | acylglycerol homeostasis | 27/7958 | 42/18723 | 3.60e-03 | 1.60e-02 | 27 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04976 | Colorectum | FAP | Bile secretion | 24/1404 | 89/8465 | 8.76e-03 | 3.21e-02 | 1.96e-02 | 24 |
| hsa049761 | Colorectum | FAP | Bile secretion | 24/1404 | 89/8465 | 8.76e-03 | 3.21e-02 | 1.96e-02 | 24 |
| hsa049762 | Liver | NAFLD | Bile secretion | 20/1043 | 89/8465 | 5.08e-03 | 4.43e-02 | 3.57e-02 | 20 |
| hsa0497611 | Liver | NAFLD | Bile secretion | 20/1043 | 89/8465 | 5.08e-03 | 4.43e-02 | 3.57e-02 | 20 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| NR1H4 | ABS | Colorectum | ADJ | SLC26A2,SLC43A2,ANPEP, etc. | 3.24e-01 |  |
| NR1H4 | HEP | Liver | HCC | AF165147.1,ADAMTSL1,MARC1, etc. | 8.18e-01 |  |
| NR1H4 | HEP | Liver | Healthy | CFH,GC,SLC13A5, etc. | 6.79e-01 |  |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| NR1H4 | SNV | Missense_Mutation | c.691N>C | p.Asp231His | p.D231H | Q96RI1 | protein_coding | tolerated(0.07) | benign(0.017) | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| NR1H4 | SNV | Missense_Mutation | rs760756841 | c.1373N>G | p.Asn458Ser | p.N458S | Q96RI1 | protein_coding | tolerated(0.33) | benign(0.037) | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| NR1H4 | SNV | Missense_Mutation | novel | c.888N>T | p.Glu296Asp | p.E296D | Q96RI1 | protein_coding | tolerated(0.48) | benign(0.003) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NR1H4 | SNV | Missense_Mutation | c.1117G>A | p.Asp373Asn | p.D373N | Q96RI1 | protein_coding | deleterious(0.01) | benign(0.087) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NR1H4 | SNV | Missense_Mutation | rs768234999 | c.1064N>T | p.Pro355Leu | p.P355L | Q96RI1 | protein_coding | tolerated(0.12) | benign(0.037) | TCGA-LD-A7W5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD |
| NR1H4 | insertion | Frame_Shift_Ins | novel | c.568_569insTTAGAAAACAAATTCACATTTTTCCT | p.Gln190LeufsTer14 | p.Q190Lfs*14 | Q96RI1 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| NR1H4 | SNV | Missense_Mutation | rs769086612 | c.367N>T | p.Arg123Cys | p.R123C | Q96RI1 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NR1H4 | SNV | Missense_Mutation | rs767846303 | c.595G>C | p.Glu199Gln | p.E199Q | Q96RI1 | protein_coding | tolerated(0.14) | benign(0.034) | TCGA-VS-A94X-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| NR1H4 | SNV | Missense_Mutation | c.1414N>T | p.Asp472Tyr | p.D472Y | Q96RI1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| NR1H4 | SNV | Missense_Mutation | c.1256N>C | p.Glu419Ala | p.E419A | Q96RI1 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | PENTACHLOROPHENOL | PENTACHLOROPHENOL | ||
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | agonist | 354702202 | TROPIFEXOR | |
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | LITHOCHOLIC ACID | LITHOCHOLIC ACID | 17963371 | |
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | agonist | 404859091 | CILOFEXOR | |
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | PMID29649907-Compound-12 | |||
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | 12-EPISCALARIN | CHEMBL269105 | 17988093 | |
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | GANODERIOL F | GANODERIOL F | 22014750 | |
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | BENZO(K)FLUORANTHENE | BENZO(K)FLUORANTHENE | ||
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | PMID29649907-Compound-11 | |||
| 9971 | NR1H4 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE, TRANSCRIPTION FACTOR | PMID29649907-Compound-8 |
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