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Gene: NR1H3 |
Gene summary for NR1H3 |
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Gene information | Species | Human | Gene symbol | NR1H3 | Gene ID | 10062 |
Gene name | nuclear receptor subfamily 1 group H member 3 | |
Gene Alias | LXR-a | |
Cytomap | 11p11.2 | |
Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q13133 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
10062 | NR1H3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 6.50e-05 | 3.62e-01 | -0.0811 |
10062 | NR1H3 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.52e-09 | 3.03e-01 | -0.1954 |
10062 | NR1H3 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.70e-04 | 2.63e-01 | -0.1526 |
10062 | NR1H3 | HTA11_696_2000001011 | Human | Colorectum | AD | 6.56e-03 | 2.53e-01 | -0.1464 |
10062 | NR1H3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.17e-07 | 2.91e-01 | -0.059 |
10062 | NR1H3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 7.77e-03 | 3.27e-01 | 0.3859 |
10062 | NR1H3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.69e-06 | 3.05e-01 | 0.3005 |
10062 | NR1H3 | LZE24T | Human | Esophagus | ESCC | 4.23e-08 | 2.22e-01 | 0.0596 |
10062 | NR1H3 | P4T-E | Human | Esophagus | ESCC | 5.92e-04 | 1.39e-01 | 0.1323 |
10062 | NR1H3 | P5T-E | Human | Esophagus | ESCC | 3.67e-07 | 4.92e-02 | 0.1327 |
10062 | NR1H3 | P8T-E | Human | Esophagus | ESCC | 3.28e-08 | 1.83e-01 | 0.0889 |
10062 | NR1H3 | P9T-E | Human | Esophagus | ESCC | 1.16e-05 | 1.65e-01 | 0.1131 |
10062 | NR1H3 | P12T-E | Human | Esophagus | ESCC | 2.22e-08 | 1.19e-01 | 0.1122 |
10062 | NR1H3 | P15T-E | Human | Esophagus | ESCC | 1.76e-04 | 1.28e-01 | 0.1149 |
10062 | NR1H3 | P16T-E | Human | Esophagus | ESCC | 7.04e-04 | 5.07e-02 | 0.1153 |
10062 | NR1H3 | P20T-E | Human | Esophagus | ESCC | 3.60e-04 | 1.29e-01 | 0.1124 |
10062 | NR1H3 | P21T-E | Human | Esophagus | ESCC | 1.30e-03 | 5.35e-02 | 0.1617 |
10062 | NR1H3 | P22T-E | Human | Esophagus | ESCC | 1.52e-11 | 1.58e-01 | 0.1236 |
10062 | NR1H3 | P24T-E | Human | Esophagus | ESCC | 3.18e-09 | 1.12e-01 | 0.1287 |
10062 | NR1H3 | P27T-E | Human | Esophagus | ESCC | 1.98e-04 | 7.77e-02 | 0.1055 |
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∗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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00192172 | Liver | HCC | regulation of fatty acid metabolic process | 53/7958 | 93/18723 | 3.36e-03 | 1.53e-02 | 53 |
GO:00458241 | Liver | HCC | negative regulation of innate immune response | 42/7958 | 71/18723 | 3.41e-03 | 1.55e-02 | 42 |
GO:00159182 | Liver | HCC | sterol transport | 71/7958 | 130/18723 | 3.49e-03 | 1.58e-02 | 71 |
GO:00550902 | Liver | HCC | acylglycerol homeostasis | 27/7958 | 42/18723 | 3.60e-03 | 1.60e-02 | 27 |
GO:00703282 | Liver | HCC | triglyceride homeostasis | 27/7958 | 42/18723 | 3.60e-03 | 1.60e-02 | 27 |
GO:00069071 | Liver | HCC | pinocytosis | 16/7958 | 22/18723 | 4.03e-03 | 1.76e-02 | 16 |
GO:0050777 | Liver | HCC | negative regulation of immune response | 101/7958 | 194/18723 | 4.40e-03 | 1.90e-02 | 101 |
GO:00512241 | Liver | HCC | negative regulation of protein transport | 69/7958 | 127/18723 | 4.67e-03 | 2.01e-02 | 69 |
GO:00712196 | Liver | HCC | cellular response to molecule of bacterial origin | 113/7958 | 221/18723 | 5.73e-03 | 2.38e-02 | 113 |
GO:0036151 | Liver | HCC | phosphatidylcholine acyl-chain remodeling | 11/7958 | 14/18723 | 6.81e-03 | 2.73e-02 | 11 |
GO:0010878 | Liver | HCC | cholesterol storage | 15/7958 | 21/18723 | 7.03e-03 | 2.80e-02 | 15 |
GO:003559212 | Liver | HCC | establishment of protein localization to extracellular region | 176/7958 | 360/18723 | 7.96e-03 | 3.15e-02 | 176 |
GO:010610611 | Liver | HCC | cold-induced thermogenesis | 76/7958 | 144/18723 | 8.07e-03 | 3.18e-02 | 76 |
GO:012016111 | Liver | HCC | regulation of cold-induced thermogenesis | 76/7958 | 144/18723 | 8.07e-03 | 3.18e-02 | 76 |
GO:00107422 | Liver | HCC | macrophage derived foam cell differentiation | 24/7958 | 38/18723 | 8.20e-03 | 3.22e-02 | 24 |
GO:00900772 | Liver | HCC | foam cell differentiation | 24/7958 | 38/18723 | 8.20e-03 | 3.22e-02 | 24 |
GO:004275211 | Liver | HCC | regulation of circadian rhythm | 65/7958 | 121/18723 | 8.25e-03 | 3.24e-02 | 65 |
GO:00603302 | Liver | HCC | regulation of response to interferon-gamma | 12/7958 | 16/18723 | 8.74e-03 | 3.40e-02 | 12 |
GO:00603342 | Liver | HCC | regulation of interferon-gamma-mediated signaling pathway | 12/7958 | 16/18723 | 8.74e-03 | 3.40e-02 | 12 |
GO:00194321 | Liver | HCC | triglyceride biosynthetic process | 26/7958 | 42/18723 | 8.76e-03 | 3.41e-02 | 26 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04932 | Colorectum | AD | Non-alcoholic fatty liver disease | 90/2092 | 155/8465 | 4.83e-19 | 1.80e-17 | 1.15e-17 | 90 |
hsa05160 | Colorectum | AD | Hepatitis C | 54/2092 | 157/8465 | 3.87e-03 | 1.96e-02 | 1.25e-02 | 54 |
hsa049321 | Colorectum | AD | Non-alcoholic fatty liver disease | 90/2092 | 155/8465 | 4.83e-19 | 1.80e-17 | 1.15e-17 | 90 |
hsa051601 | Colorectum | AD | Hepatitis C | 54/2092 | 157/8465 | 3.87e-03 | 1.96e-02 | 1.25e-02 | 54 |
hsa049322 | Colorectum | SER | Non-alcoholic fatty liver disease | 75/1580 | 155/8465 | 2.16e-17 | 5.99e-16 | 4.35e-16 | 75 |
hsa049323 | Colorectum | SER | Non-alcoholic fatty liver disease | 75/1580 | 155/8465 | 2.16e-17 | 5.99e-16 | 4.35e-16 | 75 |
hsa049324 | Colorectum | MSS | Non-alcoholic fatty liver disease | 85/1875 | 155/8465 | 4.19e-19 | 1.17e-17 | 7.17e-18 | 85 |
hsa051602 | Colorectum | MSS | Hepatitis C | 52/1875 | 157/8465 | 9.29e-04 | 5.58e-03 | 3.42e-03 | 52 |
hsa04931 | Colorectum | MSS | Insulin resistance | 36/1875 | 108/8465 | 4.74e-03 | 2.01e-02 | 1.23e-02 | 36 |
hsa049325 | Colorectum | MSS | Non-alcoholic fatty liver disease | 85/1875 | 155/8465 | 4.19e-19 | 1.17e-17 | 7.17e-18 | 85 |
hsa051603 | Colorectum | MSS | Hepatitis C | 52/1875 | 157/8465 | 9.29e-04 | 5.58e-03 | 3.42e-03 | 52 |
hsa049311 | Colorectum | MSS | Insulin resistance | 36/1875 | 108/8465 | 4.74e-03 | 2.01e-02 | 1.23e-02 | 36 |
hsa04932210 | Esophagus | ESCC | Non-alcoholic fatty liver disease | 122/4205 | 155/8465 | 5.69e-14 | 1.59e-12 | 8.14e-13 | 122 |
hsa051609 | Esophagus | ESCC | Hepatitis C | 107/4205 | 157/8465 | 1.75e-06 | 1.08e-05 | 5.55e-06 | 107 |
hsa049318 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
hsa0493238 | Esophagus | ESCC | Non-alcoholic fatty liver disease | 122/4205 | 155/8465 | 5.69e-14 | 1.59e-12 | 8.14e-13 | 122 |
hsa0516016 | Esophagus | ESCC | Hepatitis C | 107/4205 | 157/8465 | 1.75e-06 | 1.08e-05 | 5.55e-06 | 107 |
hsa0493113 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
hsa0493222 | Liver | Cirrhotic | Non-alcoholic fatty liver disease | 106/2530 | 155/8465 | 2.16e-23 | 2.40e-21 | 1.48e-21 | 106 |
hsa051605 | Liver | Cirrhotic | Hepatitis C | 63/2530 | 157/8465 | 3.67e-03 | 1.49e-02 | 9.20e-03 | 63 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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∗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. |
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Somatic mutation of malignant transformation related genes |
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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 |
NR1H3 | SNV | Missense_Mutation | novel | c.275N>G | p.Lys92Arg | p.K92R | protein_coding | tolerated(0.06) | benign(0.41) | TCGA-VS-A8EI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NR1H3 | SNV | Missense_Mutation | rs565653980 | c.776G>A | p.Arg259His | p.R259H | protein_coding | deleterious(0.05) | possibly_damaging(0.589) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
NR1H3 | SNV | Missense_Mutation | rs556085486 | c.899N>T | p.Ala300Val | p.A300V | protein_coding | deleterious(0) | benign(0.071) | TCGA-AA-A02J-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
NR1H3 | SNV | Missense_Mutation | rs778600458 | c.757C>T | p.Arg253Trp | p.R253W | protein_coding | tolerated(0.05) | benign(0.012) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
NR1H3 | SNV | Missense_Mutation | c.1327N>T | p.Pro443Ser | p.P443S | protein_coding | deleterious(0) | benign(0.322) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
NR1H3 | SNV | Missense_Mutation | rs565653980 | c.776N>A | p.Arg259His | p.R259H | protein_coding | deleterious(0.05) | possibly_damaging(0.589) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NR1H3 | SNV | Missense_Mutation | c.385N>T | p.Arg129Cys | p.R129C | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D5-6541-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
NR1H3 | SNV | Missense_Mutation | rs556085486 | c.899N>T | p.Ala300Val | p.A300V | protein_coding | deleterious(0) | benign(0.071) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD | |
NR1H3 | deletion | Frame_Shift_Del | c.271delN | p.Lys92ArgfsTer28 | p.K92Rfs*28 | protein_coding | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||||
NR1H3 | insertion | Frame_Shift_Ins | novel | c.600dupC | p.Arg201GlnfsTer31 | p.R201Qfs*31 | protein_coding | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | US9006244, E2a | |||
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | US9073931, E3 | |||
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | GSK9772 | CHEMBL493241 | 18800767,22873709 | |
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 135651391 | ||
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | T091317 | T091317 | 22579484,24480357,24268541 | |
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 375973222 | ||
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 135650789 | PAXILLINE | |
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 135649888 | ||
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | BDBM50177019 | |||
10062 | NR1H3 | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | US9006244, E2b |
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