|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: TRPT1 |
Gene summary for TRPT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRPT1 | Gene ID | 83707 |
| Gene name | tRNA phosphotransferase 1 | |
| Gene Alias | TRPT1 | |
| Cytomap | 11q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0000394 | UniProtAcc | Q86TN4 |
Top |
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 |
| 83707 | TRPT1 | LZE4T | Human | Esophagus | ESCC | 6.45e-12 | 3.31e-01 | 0.0811 |
| 83707 | TRPT1 | LZE5T | Human | Esophagus | ESCC | 5.01e-09 | 6.36e-01 | 0.0514 |
| 83707 | TRPT1 | LZE7T | Human | Esophagus | ESCC | 1.28e-05 | 5.85e-01 | 0.0667 |
| 83707 | TRPT1 | LZE8T | Human | Esophagus | ESCC | 5.49e-08 | 2.26e-01 | 0.067 |
| 83707 | TRPT1 | LZE20T | Human | Esophagus | ESCC | 5.19e-03 | 1.71e-01 | 0.0662 |
| 83707 | TRPT1 | LZE22D1 | Human | Esophagus | HGIN | 6.86e-04 | 2.59e-01 | 0.0595 |
| 83707 | TRPT1 | LZE24T | Human | Esophagus | ESCC | 1.29e-29 | 9.46e-01 | 0.0596 |
| 83707 | TRPT1 | LZE6T | Human | Esophagus | ESCC | 1.87e-09 | 5.61e-01 | 0.0845 |
| 83707 | TRPT1 | P1T-E | Human | Esophagus | ESCC | 3.86e-13 | 7.38e-01 | 0.0875 |
| 83707 | TRPT1 | P2T-E | Human | Esophagus | ESCC | 4.43e-34 | 5.12e-01 | 0.1177 |
| 83707 | TRPT1 | P4T-E | Human | Esophagus | ESCC | 6.67e-53 | 1.21e+00 | 0.1323 |
| 83707 | TRPT1 | P5T-E | Human | Esophagus | ESCC | 9.01e-26 | 4.34e-01 | 0.1327 |
| 83707 | TRPT1 | P8T-E | Human | Esophagus | ESCC | 4.83e-23 | 4.33e-01 | 0.0889 |
| 83707 | TRPT1 | P9T-E | Human | Esophagus | ESCC | 2.33e-31 | 7.03e-01 | 0.1131 |
| 83707 | TRPT1 | P10T-E | Human | Esophagus | ESCC | 1.17e-18 | 4.36e-01 | 0.116 |
| 83707 | TRPT1 | P11T-E | Human | Esophagus | ESCC | 7.11e-21 | 6.87e-01 | 0.1426 |
| 83707 | TRPT1 | P12T-E | Human | Esophagus | ESCC | 1.12e-30 | 5.68e-01 | 0.1122 |
| 83707 | TRPT1 | P15T-E | Human | Esophagus | ESCC | 3.13e-17 | 3.66e-01 | 0.1149 |
| 83707 | TRPT1 | P16T-E | Human | Esophagus | ESCC | 1.38e-27 | 6.16e-01 | 0.1153 |
| 83707 | TRPT1 | P17T-E | Human | Esophagus | ESCC | 1.13e-16 | 5.33e-01 | 0.1278 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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. |
Top |
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:000838026 | Esophagus | HGIN | RNA splicing | 160/2587 | 434/18723 | 3.74e-34 | 1.12e-30 | 160 |
| GO:003447010 | Esophagus | HGIN | ncRNA processing | 97/2587 | 395/18723 | 5.92e-09 | 3.90e-07 | 97 |
| GO:00346606 | Esophagus | HGIN | ncRNA metabolic process | 104/2587 | 485/18723 | 2.26e-06 | 8.23e-05 | 104 |
| GO:00003942 | Esophagus | HGIN | RNA splicing, via endonucleolytic cleavage and ligation | 6/2587 | 11/18723 | 1.71e-03 | 1.86e-02 | 6 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:00080333 | Esophagus | ESCC | tRNA processing | 92/8552 | 127/18723 | 7.83e-10 | 1.93e-08 | 92 |
| GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
| GO:000838012 | Liver | Cirrhotic | RNA splicing | 229/4634 | 434/18723 | 9.13e-37 | 2.86e-33 | 229 |
| GO:00344701 | Liver | Cirrhotic | ncRNA processing | 158/4634 | 395/18723 | 1.09e-11 | 6.96e-10 | 158 |
| GO:00346603 | Liver | Cirrhotic | ncRNA metabolic process | 173/4634 | 485/18723 | 3.64e-08 | 1.21e-06 | 173 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:000838022 | Liver | HCC | RNA splicing | 313/7958 | 434/18723 | 1.36e-36 | 1.73e-33 | 313 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:0008033 | Liver | HCC | tRNA processing | 87/7958 | 127/18723 | 2.66e-09 | 7.23e-08 | 87 |
| GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
| GO:000838020 | Oral cavity | OSCC | RNA splicing | 308/7305 | 434/18723 | 2.43e-42 | 7.70e-39 | 308 |
| GO:00344709 | Oral cavity | OSCC | ncRNA processing | 263/7305 | 395/18723 | 4.38e-29 | 2.78e-26 | 263 |
| GO:00346605 | Oral cavity | OSCC | ncRNA metabolic process | 296/7305 | 485/18723 | 2.94e-23 | 6.65e-21 | 296 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| TRPT1 | insertion | Nonsense_Mutation | novel | c.458_459insTCAGCCTCCCGAGTAGCTGGGATTATAG | p.His154GlnfsTer5 | p.H154Qfs*5 | Q86TN4 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| TRPT1 | SNV | Missense_Mutation | rs755471912 | c.712N>A | p.Glu238Lys | p.E238K | Q86TN4 | protein_coding | deleterious_low_confidence(0.04) | benign(0.054) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| TRPT1 | SNV | Missense_Mutation | c.232N>A | p.Val78Met | p.V78M | Q86TN4 | protein_coding | deleterious(0) | probably_damaging(0.97) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRPT1 | SNV | Missense_Mutation | rs778666111 | c.550C>G | p.Pro184Ala | p.P184A | Q86TN4 | protein_coding | tolerated(0.22) | benign(0) | TCGA-AA-A02K-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | PD |
| TRPT1 | SNV | Missense_Mutation | novel | c.106T>C | p.Ser36Pro | p.S36P | Q86TN4 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TRPT1 | SNV | Missense_Mutation | rs760406732 | c.176N>A | p.Gly59Asp | p.G59D | Q86TN4 | protein_coding | tolerated(1) | benign(0.001) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TRPT1 | SNV | Missense_Mutation | c.308A>T | p.Asn103Ile | p.N103I | Q86TN4 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRPT1 | SNV | Missense_Mutation | c.401N>T | p.Thr134Ile | p.T134I | Q86TN4 | protein_coding | deleterious(0.03) | probably_damaging(0.914) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD | |
| TRPT1 | insertion | Frame_Shift_Ins | novel | c.127_128insG | p.Ala43GlyfsTer11 | p.A43Gfs*11 | Q86TN4 | protein_coding | TCGA-DF-A2KY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD | ||
| TRPT1 | SNV | Missense_Mutation | novel | c.463N>C | p.Ile155Leu | p.I155L | Q86TN4 | protein_coding | deleterious(0.05) | benign(0.35) | TCGA-2V-A95S-01 | Liver | liver hepatocellular carcinoma | Male | Unknown | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |