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Gene: NR4A3 |
Gene summary for NR4A3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NR4A3 | Gene ID | 8013 |
| Gene name | nuclear receptor subfamily 4 group A member 3 | |
| Gene Alias | CHN | |
| Cytomap | 9q31.1 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | A0A024R168 |
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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 |
| 8013 | NR4A3 | LZE4T | Human | Esophagus | ESCC | 1.02e-02 | -1.12e-01 | 0.0811 |
| 8013 | NR4A3 | LZE5T | Human | Esophagus | ESCC | 4.92e-03 | -3.10e-02 | 0.0514 |
| 8013 | NR4A3 | LZE8T | Human | Esophagus | ESCC | 5.19e-03 | 1.17e-02 | 0.067 |
| 8013 | NR4A3 | P2T-E | Human | Esophagus | ESCC | 3.03e-05 | 1.97e-01 | 0.1177 |
| 8013 | NR4A3 | P5T-E | Human | Esophagus | ESCC | 2.48e-03 | -2.11e-01 | 0.1327 |
| 8013 | NR4A3 | P8T-E | Human | Esophagus | ESCC | 2.33e-04 | -1.50e-01 | 0.0889 |
| 8013 | NR4A3 | P12T-E | Human | Esophagus | ESCC | 4.77e-05 | -7.40e-02 | 0.1122 |
| 8013 | NR4A3 | P15T-E | Human | Esophagus | ESCC | 2.14e-03 | 2.27e-01 | 0.1149 |
| 8013 | NR4A3 | P16T-E | Human | Esophagus | ESCC | 2.38e-11 | -4.45e-02 | 0.1153 |
| 8013 | NR4A3 | P22T-E | Human | Esophagus | ESCC | 1.20e-08 | -1.60e-01 | 0.1236 |
| 8013 | NR4A3 | P23T-E | Human | Esophagus | ESCC | 7.19e-05 | -1.73e-01 | 0.108 |
| 8013 | NR4A3 | P26T-E | Human | Esophagus | ESCC | 1.22e-04 | 5.56e-02 | 0.1276 |
| 8013 | NR4A3 | P28T-E | Human | Esophagus | ESCC | 3.24e-03 | 1.08e-01 | 0.1149 |
| 8013 | NR4A3 | P31T-E | Human | Esophagus | ESCC | 8.33e-08 | -1.00e-01 | 0.1251 |
| 8013 | NR4A3 | P32T-E | Human | Esophagus | ESCC | 1.00e-04 | -2.24e-01 | 0.1666 |
| 8013 | NR4A3 | P37T-E | Human | Esophagus | ESCC | 8.16e-04 | -1.50e-01 | 0.1371 |
| 8013 | NR4A3 | P39T-E | Human | Esophagus | ESCC | 3.84e-04 | -1.48e-01 | 0.0894 |
| 8013 | NR4A3 | P47T-E | Human | Esophagus | ESCC | 1.78e-06 | 8.75e-02 | 0.1067 |
| 8013 | NR4A3 | P52T-E | Human | Esophagus | ESCC | 5.21e-09 | -1.06e-01 | 0.1555 |
| 8013 | NR4A3 | P61T-E | Human | Esophagus | ESCC | 2.87e-08 | 7.36e-02 | 0.099 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗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:0006091110 | Esophagus | ESCC | generation of precursor metabolites and energy | 331/8552 | 490/18723 | 3.86e-23 | 8.45e-21 | 331 |
| GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
| GO:0006979111 | Esophagus | ESCC | response to oxidative stress | 303/8552 | 446/18723 | 7.15e-22 | 1.30e-19 | 303 |
| GO:0045333110 | Esophagus | ESCC | cellular respiration | 173/8552 | 230/18723 | 4.53e-20 | 5.99e-18 | 173 |
| GO:0062197111 | Esophagus | ESCC | cellular response to chemical stress | 234/8552 | 337/18723 | 5.37e-19 | 5.97e-17 | 234 |
| GO:0015980110 | Esophagus | ESCC | energy derivation by oxidation of organic compounds | 220/8552 | 318/18723 | 1.20e-17 | 1.09e-15 | 220 |
| GO:0034599111 | Esophagus | ESCC | cellular response to oxidative stress | 197/8552 | 288/18723 | 3.76e-15 | 2.15e-13 | 197 |
| GO:0000302111 | Esophagus | ESCC | response to reactive oxygen species | 150/8552 | 222/18723 | 3.06e-11 | 1.02e-09 | 150 |
| GO:0030522110 | Esophagus | ESCC | intracellular receptor signaling pathway | 170/8552 | 265/18723 | 8.58e-10 | 2.09e-08 | 170 |
| GO:0042542111 | Esophagus | ESCC | response to hydrogen peroxide | 102/8552 | 146/18723 | 2.64e-09 | 5.81e-08 | 102 |
| GO:0070997111 | Esophagus | ESCC | neuron death | 216/8552 | 361/18723 | 3.49e-08 | 6.45e-07 | 216 |
| GO:0048545111 | Esophagus | ESCC | response to steroid hormone | 204/8552 | 339/18723 | 4.47e-08 | 8.11e-07 | 204 |
| GO:004578527 | Esophagus | ESCC | positive regulation of cell adhesion | 255/8552 | 437/18723 | 5.07e-08 | 9.11e-07 | 255 |
| GO:003461420 | Esophagus | ESCC | cellular response to reactive oxygen species | 103/8552 | 155/18723 | 1.34e-07 | 2.17e-06 | 103 |
| GO:0071383110 | Esophagus | ESCC | cellular response to steroid hormone stimulus | 127/8552 | 204/18723 | 1.26e-06 | 1.55e-05 | 127 |
| GO:190165319 | Esophagus | ESCC | cellular response to peptide | 208/8552 | 359/18723 | 1.68e-06 | 2.01e-05 | 208 |
| GO:00703018 | Esophagus | ESCC | cellular response to hydrogen peroxide | 68/8552 | 98/18723 | 1.70e-06 | 2.03e-05 | 68 |
| GO:1901214111 | Esophagus | ESCC | regulation of neuron death | 186/8552 | 319/18723 | 3.35e-06 | 3.73e-05 | 186 |
| GO:003109910 | Esophagus | ESCC | regeneration | 122/8552 | 198/18723 | 4.26e-06 | 4.57e-05 | 122 |
| GO:00073698 | Esophagus | ESCC | gastrulation | 115/8552 | 185/18723 | 4.35e-06 | 4.64e-05 | 115 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052028 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0520213 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
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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 |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗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 |
| NR4A3 | SNV | Missense_Mutation | c.9N>G | p.Asp3Glu | p.D3E | Q92570 | protein_coding | deleterious_low_confidence(0) | benign(0.143) | TCGA-A8-A0A6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | epirubicin | CR | |
| NR4A3 | SNV | Missense_Mutation | novel | c.1031A>G | p.Asn344Ser | p.N344S | Q92570 | protein_coding | tolerated(0.21) | probably_damaging(0.994) | TCGA-AR-A2LE-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | PD |
| NR4A3 | SNV | Missense_Mutation | rs764229734 | c.1771N>A | p.Glu591Lys | p.E591K | Q92570 | protein_coding | tolerated(0.32) | benign(0.332) | TCGA-BH-A0HU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
| NR4A3 | insertion | Frame_Shift_Ins | novel | c.1464_1465insCAAGGGACCTCAAGAGATCATCAAATCCAACCTC | p.Phe489GlnfsTer24 | p.F489Qfs*24 | Q92570 | protein_coding | TCGA-A2-A0T2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | PD | ||
| NR4A3 | insertion | Frame_Shift_Ins | novel | c.1464_1465insCAAGGGACCTCAAGAGA | p.Phe489GlnfsTer51 | p.F489Qfs*51 | Q92570 | protein_coding | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD | ||
| NR4A3 | insertion | Frame_Shift_Ins | novel | c.1464_1465insCAAGGGACCTCAAGAGA | p.Phe489GlnfsTer51 | p.F489Qfs*51 | Q92570 | protein_coding | TCGA-BH-A0BR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NR4A3 | insertion | Frame_Shift_Ins | novel | c.1464_1465insCAAGGGACCTCAAGAGATCATCAAATCCAACCTC | p.Phe489GlnfsTer24 | p.F489Qfs*24 | Q92570 | protein_coding | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| NR4A3 | deletion | Frame_Shift_Del | novel | c.987delN | p.Thr330GlnfsTer18 | p.T330Qfs*18 | Q92570 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NR4A3 | SNV | Missense_Mutation | novel | c.133N>A | p.Asp45Asn | p.D45N | Q92570 | protein_coding | deleterious(0) | probably_damaging(0.915) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NR4A3 | SNV | Missense_Mutation | c.1832N>A | p.Arg611His | p.R611H | Q92570 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| 8013 | NR4A3 | NUCLEAR HORMONE RECEPTOR, TRANSCRIPTION FACTOR, TRANSPORTER, DRUGGABLE GENOME, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE | ANTISENSE OLIGONUCLEOTIDES | 14962944 |
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