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Gene: TRIOBP |
Gene summary for TRIOBP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRIOBP | Gene ID | 11078 |
| Gene name | TRIO and F-actin binding protein | |
| Gene Alias | DFNB28 | |
| Cytomap | 22q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9H2D6 |
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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 |
| 11078 | TRIOBP | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.02e-09 | 3.30e-01 | 0.0155 |
| 11078 | TRIOBP | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.42e-21 | 7.92e-01 | -0.1808 |
| 11078 | TRIOBP | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.11e-25 | 8.70e-01 | -0.0811 |
| 11078 | TRIOBP | HTA11_78_2000001011 | Human | Colorectum | AD | 2.03e-17 | 7.52e-01 | -0.1088 |
| 11078 | TRIOBP | HTA11_347_2000001011 | Human | Colorectum | AD | 4.50e-25 | 7.48e-01 | -0.1954 |
| 11078 | TRIOBP | HTA11_411_2000001011 | Human | Colorectum | SER | 8.01e-07 | 1.13e+00 | -0.2602 |
| 11078 | TRIOBP | HTA11_2112_2000001011 | Human | Colorectum | SER | 7.38e-07 | 7.27e-01 | -0.2196 |
| 11078 | TRIOBP | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.63e-08 | 5.49e-01 | -0.1207 |
| 11078 | TRIOBP | HTA11_83_2000001011 | Human | Colorectum | SER | 1.57e-13 | 7.05e-01 | -0.1526 |
| 11078 | TRIOBP | HTA11_696_2000001011 | Human | Colorectum | AD | 9.41e-29 | 8.14e-01 | -0.1464 |
| 11078 | TRIOBP | HTA11_866_2000001011 | Human | Colorectum | AD | 2.31e-29 | 8.13e-01 | -0.1001 |
| 11078 | TRIOBP | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.51e-19 | 8.10e-01 | -0.059 |
| 11078 | TRIOBP | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.67e-08 | 6.77e-01 | -0.2061 |
| 11078 | TRIOBP | HTA11_546_2000001011 | Human | Colorectum | AD | 1.98e-10 | 7.76e-01 | -0.0842 |
| 11078 | TRIOBP | HTA11_866_3004761011 | Human | Colorectum | AD | 6.54e-21 | 6.20e-01 | 0.096 |
| 11078 | TRIOBP | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.97e-03 | 5.83e-01 | 0.0446 |
| 11078 | TRIOBP | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.06e-04 | 5.89e-01 | 0.0528 |
| 11078 | TRIOBP | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.05e-05 | 8.94e-01 | 0.0131 |
| 11078 | TRIOBP | HTA11_10623_2000001011 | Human | Colorectum | AD | 3.63e-12 | 7.97e-01 | -0.0177 |
| 11078 | TRIOBP | HTA11_10711_2000001011 | Human | Colorectum | AD | 4.94e-15 | 8.09e-01 | 0.0338 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:001063926 | Thyroid | ATC | negative regulation of organelle organization | 179/6293 | 348/18723 | 3.74e-12 | 1.50e-10 | 179 |
| GO:003253526 | Thyroid | ATC | regulation of cellular component size | 191/6293 | 383/18723 | 2.51e-11 | 8.69e-10 | 191 |
| GO:003227129 | Thyroid | ATC | regulation of protein polymerization | 127/6293 | 233/18723 | 3.64e-11 | 1.20e-09 | 127 |
| GO:0008154111 | Thyroid | ATC | actin polymerization or depolymerization | 119/6293 | 218/18723 | 1.32e-10 | 4.08e-09 | 119 |
| GO:003298422 | Thyroid | ATC | protein-containing complex disassembly | 121/6293 | 224/18723 | 2.25e-10 | 6.59e-09 | 121 |
| GO:0010811210 | Thyroid | ATC | positive regulation of cell-substrate adhesion | 73/6293 | 123/18723 | 4.12e-09 | 9.37e-08 | 73 |
| GO:0008064111 | Thyroid | ATC | regulation of actin polymerization or depolymerization | 101/6293 | 188/18723 | 9.88e-09 | 2.05e-07 | 101 |
| GO:0030832111 | Thyroid | ATC | regulation of actin filament length | 101/6293 | 189/18723 | 1.43e-08 | 2.92e-07 | 101 |
| GO:001076927 | Thyroid | ATC | regulation of cell morphogenesis involved in differentiation | 59/6293 | 96/18723 | 2.08e-08 | 4.05e-07 | 59 |
| GO:001072022 | Thyroid | ATC | positive regulation of cell development | 146/6293 | 298/18723 | 2.36e-08 | 4.56e-07 | 146 |
| GO:0030041111 | Thyroid | ATC | actin filament polymerization | 101/6293 | 191/18723 | 2.91e-08 | 5.50e-07 | 101 |
| GO:003444634 | Thyroid | ATC | substrate adhesion-dependent cell spreading | 64/6293 | 108/18723 | 3.98e-08 | 7.31e-07 | 64 |
| GO:190002427 | Thyroid | ATC | regulation of substrate adhesion-dependent cell spreading | 39/6293 | 57/18723 | 8.16e-08 | 1.41e-06 | 39 |
| GO:0030833110 | Thyroid | ATC | regulation of actin filament polymerization | 91/6293 | 172/18723 | 1.34e-07 | 2.20e-06 | 91 |
| GO:0045785210 | Thyroid | ATC | positive regulation of cell adhesion | 194/6293 | 437/18723 | 1.40e-06 | 1.75e-05 | 194 |
| GO:001077023 | Thyroid | ATC | positive regulation of cell morphogenesis involved in differentiation | 46/6293 | 79/18723 | 6.09e-06 | 6.38e-05 | 46 |
| GO:190290426 | Thyroid | ATC | negative regulation of supramolecular fiber organization | 82/6293 | 167/18723 | 2.35e-05 | 2.06e-04 | 82 |
| GO:004362412 | Thyroid | ATC | cellular protein complex disassembly | 69/6293 | 136/18723 | 2.66e-05 | 2.28e-04 | 69 |
| GO:003133333 | Thyroid | ATC | negative regulation of protein-containing complex assembly | 71/6293 | 141/18723 | 2.83e-05 | 2.38e-04 | 71 |
| GO:000206428 | Thyroid | ATC | epithelial cell development | 103/6293 | 220/18723 | 3.06e-05 | 2.55e-04 | 103 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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. |
| 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 |
| TRIOBP | SNV | Missense_Mutation | c.3142N>C | p.Glu1048Gln | p.E1048Q | Q9H2D6 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TRIOBP | SNV | Missense_Mutation | c.2179C>T | p.Arg727Trp | p.R727W | Q9H2D6 | protein_coding | deleterious_low_confidence(0.01) | benign(0.005) | TCGA-AR-A0TW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | PD | |
| TRIOBP | SNV | Missense_Mutation | c.2252N>A | p.Arg751Gln | p.R751Q | Q9H2D6 | protein_coding | tolerated_low_confidence(0.11) | benign(0.003) | TCGA-B6-A0RL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TRIOBP | SNV | Missense_Mutation | rs560619122 | c.3755N>T | p.Ser1252Phe | p.S1252F | Q9H2D6 | protein_coding | deleterious_low_confidence(0) | benign(0.117) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRIOBP | SNV | Missense_Mutation | c.1982N>A | p.Ser661Tyr | p.S661Y | Q9H2D6 | protein_coding | deleterious_low_confidence(0) | benign(0.246) | TCGA-C8-A135-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| TRIOBP | SNV | Missense_Mutation | rs572969683 | c.3218C>T | p.Ala1073Val | p.A1073V | Q9H2D6 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.861) | TCGA-E2-A153-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| TRIOBP | SNV | Missense_Mutation | novel | c.1067C>A | p.Thr356Asn | p.T356N | Q9H2D6 | protein_coding | tolerated_low_confidence(0.23) | benign(0.367) | TCGA-LD-A74U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | taxotere | SD |
| TRIOBP | SNV | Missense_Mutation | novel | c.2785C>G | p.Gln929Glu | p.Q929E | Q9H2D6 | protein_coding | deleterious_low_confidence(0) | benign(0.173) | TCGA-LL-A6FR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| TRIOBP | SNV | Missense_Mutation | novel | c.4398N>G | p.Ser1466Arg | p.S1466R | Q9H2D6 | protein_coding | tolerated_low_confidence(0.1) | benign(0) | TCGA-OL-A66P-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | CR |
| TRIOBP | insertion | Nonsense_Mutation | novel | c.939_940insGGGTAGGAACATTTGGATACAAAAAACAGGGGCTTTC | p.Ser314GlyfsTer2 | p.S314Gfs*2 | Q9H2D6 | protein_coding | TCGA-B6-A0RI-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| 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 |
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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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