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Gene: NR1H3 |
Gene summary for NR1H3 |
Gene summary. |
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 |
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 |
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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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00076232 | Colorectum | MSS | circadian rhythm | 69/3467 | 210/18723 | 4.22e-07 | 1.67e-05 | 69 |
GO:00485112 | Colorectum | MSS | rhythmic process | 89/3467 | 298/18723 | 1.17e-06 | 3.96e-05 | 89 |
GO:00507082 | Colorectum | MSS | regulation of protein secretion | 78/3467 | 268/18723 | 1.47e-05 | 3.33e-04 | 78 |
GO:00458612 | Colorectum | MSS | negative regulation of proteolysis | 97/3467 | 351/18723 | 1.57e-05 | 3.54e-04 | 97 |
GO:00093062 | Colorectum | MSS | protein secretion | 98/3467 | 359/18723 | 2.43e-05 | 5.09e-04 | 98 |
GO:00355922 | Colorectum | MSS | establishment of protein localization to extracellular region | 98/3467 | 360/18723 | 2.75e-05 | 5.58e-04 | 98 |
GO:19058972 | Colorectum | MSS | regulation of response to endoplasmic reticulum stress | 31/3467 | 82/18723 | 3.17e-05 | 6.29e-04 | 31 |
GO:00301002 | Colorectum | MSS | regulation of endocytosis | 63/3467 | 211/18723 | 4.05e-05 | 7.66e-04 | 63 |
GO:00716922 | Colorectum | MSS | protein localization to extracellular region | 99/3467 | 368/18723 | 4.17e-05 | 7.83e-04 | 99 |
GO:19016542 | Colorectum | MSS | response to ketone | 58/3467 | 194/18723 | 7.70e-05 | 1.28e-03 | 58 |
GO:00508782 | Colorectum | MSS | regulation of body fluid levels | 99/3467 | 379/18723 | 1.40e-04 | 2.07e-03 | 99 |
GO:00427522 | Colorectum | MSS | regulation of circadian rhythm | 38/3467 | 121/18723 | 4.33e-04 | 5.23e-03 | 38 |
GO:19035732 | Colorectum | MSS | negative regulation of response to endoplasmic reticulum stress | 18/3467 | 44/18723 | 4.62e-04 | 5.46e-03 | 18 |
GO:00324091 | Colorectum | MSS | regulation of transporter activity | 78/3467 | 310/18723 | 2.09e-03 | 1.78e-02 | 78 |
GO:00066312 | Colorectum | MSS | fatty acid metabolic process | 95/3467 | 390/18723 | 2.20e-03 | 1.84e-02 | 95 |
GO:00075892 | Colorectum | MSS | body fluid secretion | 29/3467 | 93/18723 | 2.21e-03 | 1.84e-02 | 29 |
GO:00620121 | Colorectum | MSS | regulation of small molecule metabolic process | 83/3467 | 334/18723 | 2.25e-03 | 1.85e-02 | 83 |
GO:00324112 | Colorectum | MSS | positive regulation of transporter activity | 35/3467 | 120/18723 | 2.95e-03 | 2.28e-02 | 35 |
GO:00226001 | Colorectum | MSS | digestive system process | 31/3467 | 104/18723 | 3.46e-03 | 2.59e-02 | 31 |
GO:00510511 | Colorectum | MSS | negative regulation of transport | 110/3467 | 470/18723 | 4.20e-03 | 3.04e-02 | 110 |
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Enriched KEGG pathways. |
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 |
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 |
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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 |
∗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 |
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 |
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 |
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 |
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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