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Gene: TRMO |
Gene summary for TRMO |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRMO | Gene ID | 51531 |
| Gene name | tRNA methyltransferase O | |
| Gene Alias | C9orf156 | |
| Cytomap | 9q22.33 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | Q5T114 |
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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 |
| 51531 | TRMO | LZE24T | Human | Esophagus | ESCC | 4.03e-02 | 1.22e-01 | 0.0596 |
| 51531 | TRMO | P1T-E | Human | Esophagus | ESCC | 9.02e-05 | 2.10e-01 | 0.0875 |
| 51531 | TRMO | P2T-E | Human | Esophagus | ESCC | 8.78e-22 | 3.81e-01 | 0.1177 |
| 51531 | TRMO | P4T-E | Human | Esophagus | ESCC | 2.73e-04 | 1.67e-01 | 0.1323 |
| 51531 | TRMO | P8T-E | Human | Esophagus | ESCC | 6.66e-07 | 9.28e-02 | 0.0889 |
| 51531 | TRMO | P9T-E | Human | Esophagus | ESCC | 4.94e-10 | 1.79e-01 | 0.1131 |
| 51531 | TRMO | P10T-E | Human | Esophagus | ESCC | 3.06e-09 | 2.00e-01 | 0.116 |
| 51531 | TRMO | P11T-E | Human | Esophagus | ESCC | 1.19e-09 | 4.17e-01 | 0.1426 |
| 51531 | TRMO | P12T-E | Human | Esophagus | ESCC | 1.45e-11 | 2.34e-01 | 0.1122 |
| 51531 | TRMO | P15T-E | Human | Esophagus | ESCC | 2.39e-11 | 2.19e-01 | 0.1149 |
| 51531 | TRMO | P16T-E | Human | Esophagus | ESCC | 3.57e-09 | 1.15e-01 | 0.1153 |
| 51531 | TRMO | P20T-E | Human | Esophagus | ESCC | 2.24e-06 | 1.29e-01 | 0.1124 |
| 51531 | TRMO | P21T-E | Human | Esophagus | ESCC | 1.08e-08 | 2.07e-01 | 0.1617 |
| 51531 | TRMO | P22T-E | Human | Esophagus | ESCC | 2.30e-04 | 1.20e-01 | 0.1236 |
| 51531 | TRMO | P23T-E | Human | Esophagus | ESCC | 8.54e-06 | 1.36e-01 | 0.108 |
| 51531 | TRMO | P24T-E | Human | Esophagus | ESCC | 3.56e-06 | 1.62e-01 | 0.1287 |
| 51531 | TRMO | P26T-E | Human | Esophagus | ESCC | 6.64e-04 | 9.69e-02 | 0.1276 |
| 51531 | TRMO | P27T-E | Human | Esophagus | ESCC | 5.41e-10 | 1.46e-01 | 0.1055 |
| 51531 | TRMO | P28T-E | Human | Esophagus | ESCC | 1.85e-10 | 2.00e-01 | 0.1149 |
| 51531 | TRMO | P30T-E | Human | Esophagus | ESCC | 2.29e-11 | 4.67e-01 | 0.137 |
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| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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: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:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| 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:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:00015101 | Esophagus | ESCC | RNA methylation | 58/8552 | 83/18723 | 6.87e-06 | 6.94e-05 | 58 |
| GO:00064002 | Esophagus | ESCC | tRNA modification | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| GO:00304881 | Esophagus | ESCC | tRNA methylation | 30/8552 | 41/18723 | 3.27e-04 | 1.93e-03 | 30 |
| 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 |
| GO:00080332 | Oral cavity | OSCC | tRNA processing | 78/7305 | 127/18723 | 2.56e-07 | 4.00e-06 | 78 |
| GO:00063991 | Oral cavity | OSCC | tRNA metabolic process | 101/7305 | 179/18723 | 1.65e-06 | 2.15e-05 | 101 |
| GO:00094511 | Oral cavity | OSCC | RNA modification | 95/7305 | 167/18723 | 2.05e-06 | 2.62e-05 | 95 |
| GO:00064001 | Oral cavity | OSCC | tRNA modification | 53/7305 | 90/18723 | 1.04e-04 | 7.70e-04 | 53 |
| GO:00434142 | Oral cavity | OSCC | macromolecule methylation | 149/7305 | 316/18723 | 1.82e-03 | 8.60e-03 | 149 |
| GO:00322591 | Oral cavity | OSCC | methylation | 168/7305 | 364/18723 | 3.03e-03 | 1.31e-02 | 168 |
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| 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 |
| TRMO | SNV | Missense_Mutation | c.1295N>A | p.Pro432His | p.P432H | Q9BU70 | protein_coding | deleterious_low_confidence(0) | benign(0.436) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRMO | SNV | Missense_Mutation | rs753673780 | c.1265N>T | p.Pro422Leu | p.P422L | Q9BU70 | protein_coding | tolerated(0.54) | benign(0.03) | TCGA-AA-3973-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Targeted Molecular therapy | bevacizumab | SD |
| TRMO | SNV | Missense_Mutation | c.984N>T | p.Trp328Cys | p.W328C | Q9BU70 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
| TRMO | SNV | Missense_Mutation | rs558175701 | c.457G>A | p.Val153Ile | p.V153I | Q9BU70 | protein_coding | tolerated(0.13) | benign(0.184) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRMO | SNV | Missense_Mutation | novel | c.846N>T | p.Glu282Asp | p.E282D | Q9BU70 | protein_coding | tolerated(0.12) | benign(0.003) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TRMO | SNV | Missense_Mutation | novel | c.523N>T | p.Asp175Tyr | p.D175Y | Q9BU70 | protein_coding | deleterious(0) | benign(0.202) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TRMO | SNV | Missense_Mutation | novel | c.400N>C | p.Lys134Gln | p.K134Q | Q9BU70 | protein_coding | deleterious(0.02) | possibly_damaging(0.604) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TRMO | SNV | Missense_Mutation | novel | c.486N>T | p.Glu162Asp | p.E162D | Q9BU70 | protein_coding | tolerated(1) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TRMO | SNV | Missense_Mutation | novel | c.503N>C | p.Asn168Thr | p.N168T | Q9BU70 | protein_coding | tolerated(0.3) | benign(0.003) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRMO | SNV | Missense_Mutation | novel | c.1093N>G | p.Phe365Val | p.F365V | Q9BU70 | protein_coding | deleterious(0.01) | possibly_damaging(0.727) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
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