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Gene: TRIO |
Gene summary for TRIO |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRIO | Gene ID | 7204 |
| Gene name | trio Rho guanine nucleotide exchange factor | |
| Gene Alias | ARHGEF23 | |
| Cytomap | 5p15.2 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O75962 |
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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 |
| 7204 | TRIO | CCI_1 | Human | Cervix | CC | 5.17e-17 | 1.46e+00 | 0.528 |
| 7204 | TRIO | CCI_2 | Human | Cervix | CC | 5.32e-14 | 1.68e+00 | 0.5249 |
| 7204 | TRIO | CCI_3 | Human | Cervix | CC | 1.84e-20 | 1.43e+00 | 0.516 |
| 7204 | TRIO | CCII_1 | Human | Cervix | CC | 7.42e-05 | 4.93e-01 | 0.3249 |
| 7204 | TRIO | HTA11_3410_2000001011 | Human | Colorectum | AD | 7.88e-11 | -3.83e-01 | 0.0155 |
| 7204 | TRIO | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.20e-05 | -4.34e-01 | -0.1808 |
| 7204 | TRIO | HTA11_347_2000001011 | Human | Colorectum | AD | 6.55e-08 | 5.41e-01 | -0.1954 |
| 7204 | TRIO | HTA11_7663_2000001011 | Human | Colorectum | SER | 7.90e-04 | 6.52e-01 | 0.0131 |
| 7204 | TRIO | HTA11_6801_2000001011 | Human | Colorectum | SER | 4.21e-03 | 2.43e-01 | 0.0171 |
| 7204 | TRIO | HTA11_6818_2000001021 | Human | Colorectum | AD | 9.96e-05 | 5.12e-01 | 0.0588 |
| 7204 | TRIO | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.47e-06 | 5.18e-01 | 0.281 |
| 7204 | TRIO | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.51e-06 | 6.49e-01 | 0.3859 |
| 7204 | TRIO | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.83e-04 | -3.28e-01 | 0.3005 |
| 7204 | TRIO | A015-C-203 | Human | Colorectum | FAP | 3.69e-30 | -5.52e-01 | -0.1294 |
| 7204 | TRIO | A015-C-204 | Human | Colorectum | FAP | 4.60e-03 | -2.52e-01 | -0.0228 |
| 7204 | TRIO | A014-C-040 | Human | Colorectum | FAP | 4.85e-02 | -1.67e-01 | -0.1184 |
| 7204 | TRIO | A002-C-201 | Human | Colorectum | FAP | 7.52e-16 | -4.33e-01 | 0.0324 |
| 7204 | TRIO | A001-C-119 | Human | Colorectum | FAP | 4.33e-09 | -4.61e-01 | -0.1557 |
| 7204 | TRIO | A001-C-108 | Human | Colorectum | FAP | 1.38e-11 | -3.11e-01 | -0.0272 |
| 7204 | TRIO | A002-C-205 | Human | Colorectum | FAP | 3.95e-30 | -5.90e-01 | -0.1236 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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:00485688 | Thyroid | ATC | embryonic organ development | 172/6293 | 427/18723 | 2.08e-03 | 9.84e-03 | 172 |
| GO:004324412 | Thyroid | ATC | regulation of protein-containing complex disassembly | 56/6293 | 121/18723 | 2.51e-03 | 1.16e-02 | 56 |
| GO:005101613 | Thyroid | ATC | barbed-end actin filament capping | 16/6293 | 26/18723 | 3.24e-03 | 1.46e-02 | 16 |
| GO:003227222 | Thyroid | ATC | negative regulation of protein polymerization | 39/6293 | 80/18723 | 3.55e-03 | 1.57e-02 | 39 |
| GO:00074113 | Thyroid | ATC | axon guidance | 96/6293 | 227/18723 | 3.74e-03 | 1.63e-02 | 96 |
| GO:00974853 | Thyroid | ATC | neuron projection guidance | 96/6293 | 228/18723 | 4.36e-03 | 1.81e-02 | 96 |
| GO:190188011 | Thyroid | ATC | negative regulation of protein depolymerization | 35/6293 | 72/18723 | 5.89e-03 | 2.37e-02 | 35 |
| GO:004559822 | Thyroid | ATC | regulation of fat cell differentiation | 61/6293 | 139/18723 | 7.28e-03 | 2.86e-02 | 61 |
| GO:0045599 | Thyroid | ATC | negative regulation of fat cell differentiation | 28/6293 | 56/18723 | 8.12e-03 | 3.13e-02 | 28 |
| GO:003083413 | Thyroid | ATC | regulation of actin filament depolymerization | 27/6293 | 54/18723 | 9.25e-03 | 3.44e-02 | 27 |
| GO:003083512 | Thyroid | ATC | negative regulation of actin filament depolymerization | 23/6293 | 45/18723 | 1.14e-02 | 4.06e-02 | 23 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ∗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 |
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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 |
| TRIO | SNV | Missense_Mutation | novel | c.1400N>A | p.Ala467Asp | p.A467D | O75962 | protein_coding | tolerated(0.06) | probably_damaging(0.994) | TCGA-A2-A0YD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| TRIO | SNV | Missense_Mutation | c.2092N>A | p.Val698Met | p.V698M | O75962 | protein_coding | deleterious(0.02) | probably_damaging(0.988) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRIO | SNV | Missense_Mutation | c.1510N>T | p.Asp504Tyr | p.D504Y | O75962 | protein_coding | deleterious(0) | possibly_damaging(0.879) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TRIO | SNV | Missense_Mutation | c.2122N>C | p.Asp708His | p.D708H | O75962 | protein_coding | tolerated(0.09) | benign(0.264) | TCGA-AC-A23C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | chemo | CR | |
| TRIO | SNV | Missense_Mutation | novel | c.4505N>A | p.Arg1502Gln | p.R1502Q | O75962 | protein_coding | deleterious(0) | probably_damaging(0.929) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TRIO | SNV | Missense_Mutation | novel | c.6510N>A | p.Phe2170Leu | p.F2170L | O75962 | protein_coding | tolerated(0.49) | benign(0.003) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TRIO | SNV | Missense_Mutation | c.5972N>C | p.Val1991Ala | p.V1991A | O75962 | protein_coding | deleterious(0) | possibly_damaging(0.474) | TCGA-AR-A1AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| TRIO | SNV | Missense_Mutation | c.8319N>A | p.Ser2773Arg | p.S2773R | O75962 | protein_coding | tolerated(0.05) | probably_damaging(0.978) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| TRIO | SNV | Missense_Mutation | rs748327260 | c.8629N>T | p.Leu2877Phe | p.L2877F | O75962 | protein_coding | tolerated(0.07) | probably_damaging(0.962) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| TRIO | SNV | Missense_Mutation | c.8104N>C | p.Val2702Leu | p.V2702L | O75962 | protein_coding | tolerated(0.07) | possibly_damaging(0.903) | TCGA-BH-A18V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| 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 |
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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 |
| Page: 1 |
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