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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 |
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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:000915017 | Endometrium | EEC | purine ribonucleotide metabolic process | 69/2168 | 368/18723 | 3.38e-05 | 5.77e-04 | 69 |
GO:007048216 | Endometrium | EEC | response to oxygen levels | 65/2168 | 347/18723 | 5.81e-05 | 9.03e-04 | 65 |
GO:004211014 | Endometrium | EEC | T cell activation | 85/2168 | 487/18723 | 6.81e-05 | 1.01e-03 | 85 |
GO:000616317 | Endometrium | EEC | purine nucleotide metabolic process | 71/2168 | 396/18723 | 1.14e-04 | 1.54e-03 | 71 |
GO:000925916 | Endometrium | EEC | ribonucleotide metabolic process | 69/2168 | 385/18723 | 1.43e-04 | 1.84e-03 | 69 |
GO:007252117 | Endometrium | EEC | purine-containing compound metabolic process | 73/2168 | 416/18723 | 1.82e-04 | 2.24e-03 | 73 |
GO:001969316 | Endometrium | EEC | ribose phosphate metabolic process | 70/2168 | 396/18723 | 1.96e-04 | 2.38e-03 | 70 |
GO:003629316 | Endometrium | EEC | response to decreased oxygen levels | 59/2168 | 322/18723 | 2.30e-04 | 2.73e-03 | 59 |
GO:007135615 | Endometrium | EEC | cellular response to tumor necrosis factor | 45/2168 | 229/18723 | 2.54e-04 | 2.94e-03 | 45 |
GO:000166616 | Endometrium | EEC | response to hypoxia | 56/2168 | 307/18723 | 3.68e-04 | 3.96e-03 | 56 |
GO:003461215 | Endometrium | EEC | response to tumor necrosis factor | 48/2168 | 253/18723 | 3.77e-04 | 4.03e-03 | 48 |
GO:004269212 | Endometrium | EEC | muscle cell differentiation | 67/2168 | 384/18723 | 3.87e-04 | 4.12e-03 | 67 |
GO:000911716 | Endometrium | EEC | nucleotide metabolic process | 80/2168 | 489/18723 | 8.65e-04 | 7.95e-03 | 80 |
GO:000675315 | Endometrium | EEC | nucleoside phosphate metabolic process | 80/2168 | 497/18723 | 1.39e-03 | 1.14e-02 | 80 |
GO:007145314 | Endometrium | EEC | cellular response to oxygen levels | 34/2168 | 177/18723 | 2.02e-03 | 1.53e-02 | 34 |
GO:00613511 | Endometrium | EEC | neural precursor cell proliferation | 29/2168 | 145/18723 | 2.24e-03 | 1.67e-02 | 29 |
GO:000941015 | Endometrium | EEC | response to xenobiotic stimulus | 73/2168 | 462/18723 | 3.55e-03 | 2.38e-02 | 73 |
GO:004620914 | Endometrium | EEC | nitric oxide metabolic process | 18/2168 | 81/18723 | 4.62e-03 | 2.97e-02 | 18 |
GO:000181913 | Endometrium | EEC | positive regulation of cytokine production | 73/2168 | 467/18723 | 4.64e-03 | 2.97e-02 | 73 |
GO:200105714 | Endometrium | EEC | reactive nitrogen species metabolic process | 18/2168 | 82/18723 | 5.29e-03 | 3.29e-02 | 18 |
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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 |
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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 |
RORA | SNV | Missense_Mutation | novel | c.1577N>G | p.Ala526Gly | p.A526G | P35398 | protein_coding | tolerated(0.48) | benign(0.365) | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD |
RORA | SNV | Missense_Mutation | c.1625A>C | p.Glu542Ala | p.E542A | P35398 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A1EN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RORA | insertion | Nonsense_Mutation | novel | c.530_531insGGGGTATGTCTGACTTTCCTCTAATGAGTTC | p.Phe178GlyfsTer4 | p.F178Gfs*4 | P35398 | protein_coding | TCGA-BH-A0HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | ||
RORA | deletion | Frame_Shift_Del | novel | c.570delN | p.Tyr190Ter | p.Y190* | P35398 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
RORA | SNV | Missense_Mutation | c.691N>A | p.Asp231Asn | p.D231N | P35398 | protein_coding | tolerated(0.25) | benign(0.001) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
RORA | SNV | Missense_Mutation | c.618G>C | p.Gln206His | p.Q206H | P35398 | protein_coding | tolerated(0.06) | benign(0.015) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD | |
RORA | SNV | Missense_Mutation | c.1162C>A | p.Leu388Ile | p.L388I | P35398 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
RORA | SNV | Missense_Mutation | novel | c.1567N>T | p.Ala523Ser | p.A523S | P35398 | protein_coding | tolerated(0.45) | benign(0.323) | TCGA-AA-A02W-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
RORA | SNV | Missense_Mutation | c.467N>G | p.Asn156Ser | p.N156S | P35398 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RORA | SNV | Missense_Mutation | novel | c.947C>T | p.Ser316Leu | p.S316L | P35398 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | 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 |
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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