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Gene: TRMU |
Gene summary for TRMU |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRMU | Gene ID | 55687 |
| Gene name | tRNA mitochondrial 2-thiouridylase | |
| Gene Alias | LCAL3 | |
| Cytomap | 22q13.31 | |
| Gene Type | protein-coding | GO ID | GO:0002097 | UniProtAcc | Q2PPL5 |
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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 |
| 55687 | TRMU | LZE2T | Human | Esophagus | ESCC | 4.73e-03 | 2.87e-01 | 0.082 |
| 55687 | TRMU | LZE4T | Human | Esophagus | ESCC | 3.18e-05 | 1.51e-01 | 0.0811 |
| 55687 | TRMU | LZE7T | Human | Esophagus | ESCC | 8.50e-13 | 4.55e-01 | 0.0667 |
| 55687 | TRMU | LZE20T | Human | Esophagus | ESCC | 1.26e-02 | 1.09e-01 | 0.0662 |
| 55687 | TRMU | LZE22D1 | Human | Esophagus | HGIN | 5.14e-03 | 1.41e-01 | 0.0595 |
| 55687 | TRMU | LZE24T | Human | Esophagus | ESCC | 6.88e-12 | 2.38e-01 | 0.0596 |
| 55687 | TRMU | LZE6T | Human | Esophagus | ESCC | 5.26e-07 | 2.90e-01 | 0.0845 |
| 55687 | TRMU | P1T-E | Human | Esophagus | ESCC | 3.58e-07 | 2.56e-01 | 0.0875 |
| 55687 | TRMU | P2T-E | Human | Esophagus | ESCC | 6.68e-12 | 2.30e-01 | 0.1177 |
| 55687 | TRMU | P4T-E | Human | Esophagus | ESCC | 2.11e-11 | 2.33e-01 | 0.1323 |
| 55687 | TRMU | P5T-E | Human | Esophagus | ESCC | 4.64e-08 | 1.54e-01 | 0.1327 |
| 55687 | TRMU | P8T-E | Human | Esophagus | ESCC | 8.87e-11 | 1.75e-01 | 0.0889 |
| 55687 | TRMU | P9T-E | Human | Esophagus | ESCC | 1.88e-05 | 1.34e-01 | 0.1131 |
| 55687 | TRMU | P10T-E | Human | Esophagus | ESCC | 6.38e-24 | 4.32e-01 | 0.116 |
| 55687 | TRMU | P11T-E | Human | Esophagus | ESCC | 3.66e-11 | 3.55e-01 | 0.1426 |
| 55687 | TRMU | P12T-E | Human | Esophagus | ESCC | 8.51e-17 | 3.20e-01 | 0.1122 |
| 55687 | TRMU | P15T-E | Human | Esophagus | ESCC | 1.52e-21 | 3.69e-01 | 0.1149 |
| 55687 | TRMU | P16T-E | Human | Esophagus | ESCC | 6.24e-22 | 4.12e-01 | 0.1153 |
| 55687 | TRMU | P17T-E | Human | Esophagus | ESCC | 8.50e-05 | 2.01e-01 | 0.1278 |
| 55687 | TRMU | P19T-E | Human | Esophagus | ESCC | 6.53e-04 | 2.93e-01 | 0.1662 |
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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 | ||
| 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 |
| ∗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: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: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:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:00064002 | Esophagus | ESCC | tRNA modification | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| 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:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
| GO:0006400 | Liver | HCC | tRNA modification | 60/7958 | 90/18723 | 3.09e-06 | 4.09e-05 | 60 |
| 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 |
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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 |
| TRMU | SNV | Missense_Mutation | novel | c.88C>A | p.Gln30Lys | p.Q30K | O75648 | protein_coding | tolerated(0.23) | benign(0.017) | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| TRMU | SNV | Missense_Mutation | c.334N>T | p.His112Tyr | p.H112Y | O75648 | protein_coding | deleterious(0.02) | benign(0.279) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TRMU | SNV | Missense_Mutation | novel | c.395N>T | p.Ser132Phe | p.S132F | O75648 | protein_coding | deleterious(0) | probably_damaging(0.971) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRMU | SNV | Missense_Mutation | rs202229063 | c.1001G>A | p.Arg334His | p.R334H | O75648 | protein_coding | deleterious(0.05) | benign(0.4) | TCGA-E2-A1IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| TRMU | insertion | In_Frame_Ins | novel | c.398_399insCCTAGGTGGCTGGCTGTCAGGCAC | p.Leu133_Glu134insLeuGlyGlyTrpLeuSerGlyThr | p.L133_E134insLGGWLSGT | O75648 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| TRMU | insertion | Frame_Shift_Ins | novel | c.394_395insTTCTTCAACTGTTTCTGTACAGTAAAAA | p.Ser132PhefsTer14 | p.S132Ffs*14 | O75648 | protein_coding | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TRMU | deletion | Frame_Shift_Del | novel | c.100delG | p.Val34CysfsTer3 | p.V34Cfs*3 | O75648 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TRMU | SNV | Missense_Mutation | c.108N>A | p.Met36Ile | p.M36I | O75648 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| TRMU | SNV | Missense_Mutation | c.334N>T | p.His112Tyr | p.H112Y | O75648 | protein_coding | deleterious(0.02) | benign(0.279) | TCGA-MU-A51Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| TRMU | SNV | Missense_Mutation | rs773745635 | c.880N>T | p.Arg294Trp | p.R294W | O75648 | protein_coding | deleterious(0) | possibly_damaging(0.806) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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