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Gene: NR4A2 |
Gene summary for NR4A2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NR4A2 | Gene ID | 4929 |
Gene name | nuclear receptor subfamily 4 group A member 2 | |
Gene Alias | HZF-3 | |
Cytomap | 2q24.1 | |
Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | F1D8N6 |
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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 |
4929 | NR4A2 | GSM4909282 | Human | Breast | IDC | 2.79e-12 | 6.24e-01 | -0.0288 |
4929 | NR4A2 | GSM4909286 | Human | Breast | IDC | 5.57e-04 | 1.19e-01 | 0.1081 |
4929 | NR4A2 | GSM4909291 | Human | Breast | IDC | 2.96e-03 | 3.82e-01 | 0.1753 |
4929 | NR4A2 | GSM4909294 | Human | Breast | IDC | 2.27e-02 | -2.11e-01 | 0.2022 |
4929 | NR4A2 | GSM4909297 | Human | Breast | IDC | 7.30e-03 | -1.60e-01 | 0.1517 |
4929 | NR4A2 | GSM4909298 | Human | Breast | IDC | 2.71e-02 | -2.30e-01 | 0.1551 |
4929 | NR4A2 | GSM4909304 | Human | Breast | IDC | 2.07e-02 | -2.05e-01 | 0.1636 |
4929 | NR4A2 | GSM4909308 | Human | Breast | IDC | 2.11e-34 | 7.85e-01 | 0.158 |
4929 | NR4A2 | GSM4909311 | Human | Breast | IDC | 6.16e-11 | -2.79e-01 | 0.1534 |
4929 | NR4A2 | GSM4909313 | Human | Breast | IDC | 3.13e-02 | 3.03e-01 | 0.0391 |
4929 | NR4A2 | GSM4909319 | Human | Breast | IDC | 1.90e-09 | -2.39e-01 | 0.1563 |
4929 | NR4A2 | GSM4909320 | Human | Breast | IDC | 4.54e-03 | -3.17e-01 | 0.1575 |
4929 | NR4A2 | GSM4909321 | Human | Breast | IDC | 3.04e-03 | -2.14e-01 | 0.1559 |
4929 | NR4A2 | brca1 | Human | Breast | Precancer | 4.83e-06 | -2.88e-01 | -0.0338 |
4929 | NR4A2 | brca2 | Human | Breast | Precancer | 1.56e-05 | -2.67e-01 | -0.024 |
4929 | NR4A2 | brca3 | Human | Breast | Precancer | 1.10e-04 | -2.82e-01 | -0.0263 |
4929 | NR4A2 | brca10 | Human | Breast | Precancer | 1.20e-05 | -2.88e-01 | -0.0029 |
4929 | NR4A2 | NCCBC14 | Human | Breast | DCIS | 1.73e-06 | -2.86e-01 | 0.2021 |
4929 | NR4A2 | NCCBC3 | Human | Breast | DCIS | 1.44e-04 | -2.62e-01 | 0.1198 |
4929 | NR4A2 | NCCBC5 | Human | Breast | DCIS | 2.45e-04 | -1.96e-01 | 0.2046 |
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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:00219556 | Thyroid | PTC | central nervous system neuron axonogenesis | 19/5968 | 35/18723 | 4.94e-03 | 2.29e-02 | 19 |
GO:00309007 | Thyroid | PTC | forebrain development | 143/5968 | 379/18723 | 8.47e-03 | 3.56e-02 | 143 |
GO:200123335 | Thyroid | ATC | regulation of apoptotic signaling pathway | 206/6293 | 356/18723 | 2.81e-21 | 5.92e-19 | 206 |
GO:000697934 | Thyroid | ATC | response to oxidative stress | 246/6293 | 446/18723 | 2.98e-21 | 6.09e-19 | 246 |
GO:007048228 | Thyroid | ATC | response to oxygen levels | 193/6293 | 347/18723 | 1.83e-17 | 1.93e-15 | 193 |
GO:006219734 | Thyroid | ATC | cellular response to chemical stress | 188/6293 | 337/18723 | 3.16e-17 | 3.07e-15 | 188 |
GO:001605525 | Thyroid | ATC | Wnt signaling pathway | 234/6293 | 444/18723 | 4.64e-17 | 4.31e-15 | 234 |
GO:019873825 | Thyroid | ATC | cell-cell signaling by wnt | 234/6293 | 446/18723 | 9.26e-17 | 8.25e-15 | 234 |
GO:003629328 | Thyroid | ATC | response to decreased oxygen levels | 177/6293 | 322/18723 | 1.81e-15 | 1.32e-13 | 177 |
GO:000166628 | Thyroid | ATC | response to hypoxia | 169/6293 | 307/18723 | 6.58e-15 | 4.12e-13 | 169 |
GO:003459934 | Thyroid | ATC | cellular response to oxidative stress | 158/6293 | 288/18723 | 7.35e-14 | 3.94e-12 | 158 |
GO:2001234210 | Thyroid | ATC | negative regulation of apoptotic signaling pathway | 129/6293 | 224/18723 | 1.26e-13 | 6.46e-12 | 129 |
GO:0071496210 | Thyroid | ATC | cellular response to external stimulus | 165/6293 | 320/18723 | 2.01e-11 | 7.23e-10 | 165 |
GO:006007025 | Thyroid | ATC | canonical Wnt signaling pathway | 154/6293 | 303/18723 | 3.68e-10 | 1.02e-08 | 154 |
GO:006156423 | Thyroid | ATC | axon development | 220/6293 | 467/18723 | 6.85e-10 | 1.80e-08 | 220 |
GO:0070997210 | Thyroid | ATC | neuron death | 176/6293 | 361/18723 | 1.43e-09 | 3.57e-08 | 176 |
GO:000740919 | Thyroid | ATC | axonogenesis | 197/6293 | 418/18723 | 5.09e-09 | 1.13e-07 | 197 |
GO:190165325 | Thyroid | ATC | cellular response to peptide | 173/6293 | 359/18723 | 5.87e-09 | 1.28e-07 | 173 |
GO:0030522112 | Thyroid | ATC | intracellular receptor signaling pathway | 134/6293 | 265/18723 | 7.58e-09 | 1.63e-07 | 134 |
GO:190121428 | Thyroid | ATC | regulation of neuron death | 156/6293 | 319/18723 | 9.30e-09 | 1.96e-07 | 156 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0492812 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
hsa0492813 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
hsa0492816 | Esophagus | ESCC | Parathyroid hormone synthesis, secretion and action | 66/4205 | 106/8465 | 5.86e-03 | 1.47e-02 | 7.51e-03 | 66 |
hsa0492817 | Esophagus | ESCC | Parathyroid hormone synthesis, secretion and action | 66/4205 | 106/8465 | 5.86e-03 | 1.47e-02 | 7.51e-03 | 66 |
hsa0492810 | Lung | IAC | Parathyroid hormone synthesis, secretion and action | 26/1053 | 106/8465 | 4.34e-04 | 4.03e-03 | 2.68e-03 | 26 |
hsa0492811 | Lung | IAC | Parathyroid hormone synthesis, secretion and action | 26/1053 | 106/8465 | 4.34e-04 | 4.03e-03 | 2.68e-03 | 26 |
hsa0492814 | Prostate | BPH | Parathyroid hormone synthesis, secretion and action | 33/1718 | 106/8465 | 5.30e-03 | 1.75e-02 | 1.08e-02 | 33 |
hsa0492815 | Prostate | BPH | Parathyroid hormone synthesis, secretion and action | 33/1718 | 106/8465 | 5.30e-03 | 1.75e-02 | 1.08e-02 | 33 |
hsa0492822 | Prostate | Tumor | Parathyroid hormone synthesis, secretion and action | 35/1791 | 106/8465 | 2.89e-03 | 1.07e-02 | 6.67e-03 | 35 |
hsa0492832 | Prostate | Tumor | Parathyroid hormone synthesis, secretion and action | 35/1791 | 106/8465 | 2.89e-03 | 1.07e-02 | 6.67e-03 | 35 |
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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 |
NR4A2 | SNV | Missense_Mutation | c.1028G>T | p.Gly343Val | p.G343V | P43354 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
NR4A2 | SNV | Missense_Mutation | novel | c.872N>C | p.Val291Ala | p.V291A | P43354 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD |
NR4A2 | deletion | Frame_Shift_Del | c.430delG | p.Asp144ThrfsTer19 | p.D144Tfs*19 | P43354 | protein_coding | TCGA-E2-A1IF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |||
NR4A2 | SNV | Missense_Mutation | c.833G>T | p.Arg278Leu | p.R278L | P43354 | protein_coding | deleterious(0.01) | probably_damaging(0.92) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NR4A2 | SNV | Missense_Mutation | c.52G>A | p.Ala18Thr | p.A18T | P43354 | protein_coding | deleterious(0.03) | possibly_damaging(0.656) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NR4A2 | SNV | Missense_Mutation | c.16N>A | p.Ala6Thr | p.A6T | P43354 | protein_coding | tolerated(0.33) | benign(0.339) | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | |
NR4A2 | SNV | Missense_Mutation | c.866N>A | p.Arg289His | p.R289H | P43354 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NR4A2 | SNV | Missense_Mutation | novel | c.503C>T | p.Thr168Met | p.T168M | P43354 | protein_coding | deleterious(0.03) | benign(0.11) | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
NR4A2 | SNV | Missense_Mutation | novel | c.1145N>G | p.Leu382Arg | p.L382R | P43354 | protein_coding | deleterious(0.01) | benign(0.436) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
NR4A2 | SNV | Missense_Mutation | novel | c.214N>A | p.Asp72Asn | p.D72N | P43354 | protein_coding | tolerated(0.07) | probably_damaging(0.932) | TCGA-AZ-4315-01 | 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 |
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