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Gene: RORA |
Gene summary for RORA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RORA | Gene ID | 6095 |
| Gene name | RAR related orphan receptor A | |
| Gene Alias | IDDECA | |
| Cytomap | 15q22.2 | |
| Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | A0A0C4DFP5 |
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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 |
| 6095 | RORA | CCI_2 | Human | Cervix | CC | 2.10e-10 | 9.47e-01 | 0.5249 |
| 6095 | RORA | CCI_3 | Human | Cervix | CC | 3.59e-17 | 1.06e+00 | 0.516 |
| 6095 | RORA | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.57e-08 | -4.59e-01 | 0.0155 |
| 6095 | RORA | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.14e-02 | -4.31e-01 | -0.1808 |
| 6095 | RORA | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.29e-04 | -4.13e-01 | -0.1207 |
| 6095 | RORA | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.40e-07 | -4.37e-01 | -0.059 |
| 6095 | RORA | HTA11_866_3004761011 | Human | Colorectum | AD | 8.56e-12 | -5.68e-01 | 0.096 |
| 6095 | RORA | HTA11_7663_2000001011 | Human | Colorectum | SER | 1.42e-02 | 9.58e-01 | 0.0131 |
| 6095 | RORA | HTA11_7696_3000711011 | Human | Colorectum | AD | 8.51e-13 | -5.62e-01 | 0.0674 |
| 6095 | RORA | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.43e-03 | -5.05e-01 | 0.0588 |
| 6095 | RORA | HTA11_99999970781_79442 | Human | Colorectum | MSS | 8.77e-17 | -5.84e-01 | 0.294 |
| 6095 | RORA | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.75e-03 | -2.39e-01 | 0.3859 |
| 6095 | RORA | HTA11_99999974143_84620 | Human | Colorectum | MSS | 6.01e-09 | -6.17e-02 | 0.3005 |
| 6095 | RORA | F007 | Human | Colorectum | FAP | 3.44e-02 | -4.44e-01 | 0.1176 |
| 6095 | RORA | A015-C-203 | Human | Colorectum | FAP | 3.53e-02 | -1.30e-01 | -0.1294 |
| 6095 | RORA | A002-C-201 | Human | Colorectum | FAP | 2.14e-10 | -5.12e-01 | 0.0324 |
| 6095 | RORA | A002-C-203 | Human | Colorectum | FAP | 1.27e-03 | -3.39e-01 | 0.2786 |
| 6095 | RORA | A002-C-205 | Human | Colorectum | FAP | 4.66e-08 | -4.46e-01 | -0.1236 |
| 6095 | RORA | A015-C-006 | Human | Colorectum | FAP | 1.70e-05 | -4.51e-01 | -0.0994 |
| 6095 | RORA | A015-C-202 | Human | Colorectum | FAP | 1.53e-03 | 4.01e-01 | -0.0849 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00421108 | Cervix | CC | T cell activation | 107/2311 | 487/18723 | 1.24e-09 | 1.46e-07 | 107 |
| GO:00018197 | Cervix | CC | positive regulation of cytokine production | 95/2311 | 467/18723 | 4.88e-07 | 1.85e-05 | 95 |
| GO:00305229 | Cervix | CC | intracellular receptor signaling pathway | 60/2311 | 265/18723 | 1.89e-06 | 5.97e-05 | 60 |
| GO:00485118 | Cervix | CC | rhythmic process | 65/2311 | 298/18723 | 2.79e-06 | 8.04e-05 | 65 |
| GO:00454445 | Cervix | CC | fat cell differentiation | 53/2311 | 229/18723 | 3.72e-06 | 9.75e-05 | 53 |
| GO:00346129 | Cervix | CC | response to tumor necrosis factor | 55/2311 | 253/18723 | 1.75e-05 | 3.32e-04 | 55 |
| GO:00713569 | Cervix | CC | cellular response to tumor necrosis factor | 51/2311 | 229/18723 | 1.75e-05 | 3.32e-04 | 51 |
| GO:00507273 | Cervix | CC | regulation of inflammatory response | 75/2311 | 386/18723 | 3.95e-05 | 6.18e-04 | 75 |
| GO:00431228 | Cervix | CC | regulation of I-kappaB kinase/NF-kappaB signaling | 53/2311 | 249/18723 | 4.50e-05 | 6.87e-04 | 53 |
| GO:00076238 | Cervix | CC | circadian rhythm | 46/2311 | 210/18723 | 6.76e-05 | 9.60e-04 | 46 |
| GO:000166610 | Cervix | CC | response to hypoxia | 61/2311 | 307/18723 | 1.04e-04 | 1.34e-03 | 61 |
| GO:007048210 | Cervix | CC | response to oxygen levels | 67/2311 | 347/18723 | 1.21e-04 | 1.51e-03 | 67 |
| GO:00072497 | Cervix | CC | I-kappaB kinase/NF-kappaB signaling | 56/2311 | 281/18723 | 1.81e-04 | 2.12e-03 | 56 |
| GO:003629310 | Cervix | CC | response to decreased oxygen levels | 62/2311 | 322/18723 | 2.29e-04 | 2.57e-03 | 62 |
| GO:00302173 | Cervix | CC | T cell differentiation | 51/2311 | 257/18723 | 3.81e-04 | 3.89e-03 | 51 |
| GO:00714539 | Cervix | CC | cellular response to oxygen levels | 38/2311 | 177/18723 | 4.23e-04 | 4.27e-03 | 38 |
| GO:00196939 | Cervix | CC | ribose phosphate metabolic process | 72/2311 | 396/18723 | 4.49e-04 | 4.48e-03 | 72 |
| GO:00092599 | Cervix | CC | ribonucleotide metabolic process | 70/2311 | 385/18723 | 5.35e-04 | 5.18e-03 | 70 |
| GO:00362949 | Cervix | CC | cellular response to decreased oxygen levels | 35/2311 | 161/18723 | 5.49e-04 | 5.29e-03 | 35 |
| GO:19031314 | Cervix | CC | mononuclear cell differentiation | 76/2311 | 426/18723 | 5.66e-04 | 5.42e-03 | 76 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501716 | Cervix | CC | Spinocerebellar ataxia | 35/1267 | 143/8465 | 1.77e-03 | 7.21e-03 | 4.26e-03 | 35 |
| hsa046596 | Cervix | CC | Th17 cell differentiation | 28/1267 | 108/8465 | 1.99e-03 | 7.98e-03 | 4.72e-03 | 28 |
| hsa0501717 | Cervix | CC | Spinocerebellar ataxia | 35/1267 | 143/8465 | 1.77e-03 | 7.21e-03 | 4.26e-03 | 35 |
| hsa0465911 | Cervix | CC | Th17 cell differentiation | 28/1267 | 108/8465 | 1.99e-03 | 7.98e-03 | 4.72e-03 | 28 |
| hsa05017 | Colorectum | AD | Spinocerebellar ataxia | 60/2092 | 143/8465 | 3.78e-06 | 4.35e-05 | 2.78e-05 | 60 |
| hsa050171 | Colorectum | AD | Spinocerebellar ataxia | 60/2092 | 143/8465 | 3.78e-06 | 4.35e-05 | 2.78e-05 | 60 |
| hsa050172 | Colorectum | SER | Spinocerebellar ataxia | 46/1580 | 143/8465 | 6.78e-05 | 7.51e-04 | 5.45e-04 | 46 |
| hsa050173 | Colorectum | SER | Spinocerebellar ataxia | 46/1580 | 143/8465 | 6.78e-05 | 7.51e-04 | 5.45e-04 | 46 |
| hsa050174 | Colorectum | MSS | Spinocerebellar ataxia | 60/1875 | 143/8465 | 7.14e-08 | 1.26e-06 | 7.71e-07 | 60 |
| hsa050175 | Colorectum | MSS | Spinocerebellar ataxia | 60/1875 | 143/8465 | 7.14e-08 | 1.26e-06 | 7.71e-07 | 60 |
| hsa050178 | Colorectum | FAP | Spinocerebellar ataxia | 37/1404 | 143/8465 | 2.94e-03 | 1.29e-02 | 7.86e-03 | 37 |
| hsa050179 | Colorectum | FAP | Spinocerebellar ataxia | 37/1404 | 143/8465 | 2.94e-03 | 1.29e-02 | 7.86e-03 | 37 |
| hsa0501718 | Endometrium | AEH | Spinocerebellar ataxia | 43/1197 | 143/8465 | 5.92e-07 | 7.69e-06 | 5.63e-06 | 43 |
| hsa0501719 | Endometrium | AEH | Spinocerebellar ataxia | 43/1197 | 143/8465 | 5.92e-07 | 7.69e-06 | 5.63e-06 | 43 |
| hsa0501723 | Endometrium | EEC | Spinocerebellar ataxia | 43/1237 | 143/8465 | 1.46e-06 | 2.01e-05 | 1.50e-05 | 43 |
| hsa0501733 | Endometrium | EEC | Spinocerebellar ataxia | 43/1237 | 143/8465 | 1.46e-06 | 2.01e-05 | 1.50e-05 | 43 |
| hsa0501727 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
| hsa05017112 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
| hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa046599 | Esophagus | ESCC | Th17 cell differentiation | 68/4205 | 108/8465 | 3.53e-03 | 9.30e-03 | 4.76e-03 | 68 |
| Page: 1 2 3 |
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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 |
| RORA | BAS | Breast | DCIS | PLIN2,SERPINE1,BNIP3L, etc. | 1.27e-01 |  |
| RORA | CD8TCM | Breast | ADJ | IL7R,KLRB1,SARAF, etc. | 5.13e-01 |  |
| RORA | CD8TEXINT | Breast | DCIS | IL7R,KLRB1,SARAF, etc. | 1.57e-01 | |
| RORA | CD4TN | Breast | DCIS | IL7R,KLRB1,SARAF, etc. | 2.50e-01 | |
| RORA | TREG | Breast | DCIS | IL7R,KLRB1,SARAF, etc. | 1.55e-01 | |
| RORA | TH17 | Breast | DCIS | IL7R,KLRB1,SARAF, etc. | 4.51e-02 | |
| RORA | CD8TEXINT | Breast | Healthy | IL7R,KLRB1,SARAF, etc. | 1.28e-01 |  |
| RORA | CD8TCM | Breast | Healthy | IL7R,KLRB1,SARAF, etc. | 1.72e-01 | |
| RORA | TREG | Breast | Healthy | IL7R,KLRB1,SARAF, etc. | 4.97e-02 | |
| RORA | TREG | Breast | IDC | IL7R,KLRB1,SARAF, etc. | 1.66e-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 2 3 4 5 6 7 8 9 10 11 |
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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 |
| RORA | SNV | Missense_Mutation | c.95G>C | p.Arg32Thr | p.R32T | P35398 | protein_coding | tolerated_low_confidence(0.07) | benign(0.011) | TCGA-18-3416-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RORA | SNV | Missense_Mutation | novel | c.68N>C | p.Gly23Ala | p.G23A | P35398 | protein_coding | deleterious_low_confidence(0) | benign(0.023) | TCGA-43-A474-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | CR |
| RORA | SNV | Missense_Mutation | novel | c.895C>A | p.Pro299Thr | p.P299T | P35398 | protein_coding | deleterious(0.03) | benign(0.327) | TCGA-46-3768-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Chemotherapy | carboplatin | SD |
| RORA | SNV | Missense_Mutation | novel | c.1544G>C | p.Gly515Ala | p.G515A | P35398 | protein_coding | tolerated(0.53) | benign(0.033) | TCGA-56-1622-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| RORA | SNV | Missense_Mutation | novel | c.832N>A | p.Cys278Ser | p.C278S | P35398 | protein_coding | tolerated(0.33) | possibly_damaging(0.497) | TCGA-77-7141-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RORA | SNV | Missense_Mutation | novel | c.977A>G | p.Glu326Gly | p.E326G | P35398 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-90-7964-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RORA | SNV | Missense_Mutation | novel | c.1663G>A | p.Asp555Asn | p.D555N | P35398 | protein_coding | deleterious_low_confidence(0) | benign(0.411) | TCGA-O2-A52Q-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| RORA | SNV | Missense_Mutation | novel | c.1199N>A | p.Arg400Lys | p.R400K | P35398 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-CR-6472-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | paclitaxel | SD |
| RORA | SNV | Missense_Mutation | novel | c.1634C>G | p.Thr545Ser | p.T545S | P35398 | protein_coding | tolerated(1) | benign(0.028) | TCGA-F7-A50J-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR |
| RORA | SNV | Missense_Mutation | novel | c.291N>A | p.Met97Ile | p.M97I | P35398 | protein_coding | tolerated(0.55) | benign(0.001) | TCGA-F7-A623-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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 |
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | interferon beta-1a | 31649263 | ||
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | agonist | 381118853 | ||
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | agonist | 135651223 | T091317 | |
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | agonist | 135651457 | CHOLESTEROL | |
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | citalopram | CITALOPRAM | 19846067 | |
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | agonist | 135651458 | ||
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | agonist | 178100434 | ||
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | agonist | 310264687 | ||
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | T091317 | T091317 | ||
| 6095 | RORA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR, KINASE | US9598431, 3 |
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