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Gene: TRMT61A |
Gene summary for TRMT61A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRMT61A | Gene ID | 115708 |
| Gene name | tRNA methyltransferase 61A | |
| Gene Alias | C14orf172 | |
| Cytomap | 14q32.33 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | A0A024R6Q2 |
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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 |
| 115708 | TRMT61A | LZE7T | Human | Esophagus | ESCC | 2.93e-04 | 1.34e-01 | 0.0667 |
| 115708 | TRMT61A | LZE20T | Human | Esophagus | ESCC | 4.34e-06 | 1.57e-01 | 0.0662 |
| 115708 | TRMT61A | LZE22T | Human | Esophagus | ESCC | 2.11e-05 | 3.79e-01 | 0.068 |
| 115708 | TRMT61A | LZE24T | Human | Esophagus | ESCC | 8.10e-10 | 2.81e-01 | 0.0596 |
| 115708 | TRMT61A | P1T-E | Human | Esophagus | ESCC | 7.66e-03 | 1.80e-01 | 0.0875 |
| 115708 | TRMT61A | P2T-E | Human | Esophagus | ESCC | 6.34e-14 | 1.35e-01 | 0.1177 |
| 115708 | TRMT61A | P4T-E | Human | Esophagus | ESCC | 2.23e-10 | 3.14e-01 | 0.1323 |
| 115708 | TRMT61A | P5T-E | Human | Esophagus | ESCC | 2.75e-28 | 5.62e-01 | 0.1327 |
| 115708 | TRMT61A | P8T-E | Human | Esophagus | ESCC | 2.82e-07 | 1.56e-01 | 0.0889 |
| 115708 | TRMT61A | P9T-E | Human | Esophagus | ESCC | 1.52e-05 | 1.73e-01 | 0.1131 |
| 115708 | TRMT61A | P10T-E | Human | Esophagus | ESCC | 4.55e-45 | 8.15e-01 | 0.116 |
| 115708 | TRMT61A | P11T-E | Human | Esophagus | ESCC | 7.49e-04 | 3.01e-01 | 0.1426 |
| 115708 | TRMT61A | P12T-E | Human | Esophagus | ESCC | 1.74e-17 | 3.55e-01 | 0.1122 |
| 115708 | TRMT61A | P15T-E | Human | Esophagus | ESCC | 4.38e-23 | 5.64e-01 | 0.1149 |
| 115708 | TRMT61A | P16T-E | Human | Esophagus | ESCC | 1.09e-24 | 3.21e-01 | 0.1153 |
| 115708 | TRMT61A | P17T-E | Human | Esophagus | ESCC | 3.44e-09 | 6.64e-01 | 0.1278 |
| 115708 | TRMT61A | P19T-E | Human | Esophagus | ESCC | 3.70e-02 | 2.84e-01 | 0.1662 |
| 115708 | TRMT61A | P20T-E | Human | Esophagus | ESCC | 1.27e-11 | 3.24e-01 | 0.1124 |
| 115708 | TRMT61A | P21T-E | Human | Esophagus | ESCC | 1.63e-23 | 4.06e-01 | 0.1617 |
| 115708 | TRMT61A | P22T-E | Human | Esophagus | ESCC | 3.11e-13 | 1.80e-01 | 0.1236 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00800092 | Esophagus | ESCC | mRNA methylation | 14/8552 | 16/18723 | 6.78e-04 | 3.56e-03 | 14 |
| GO:00165561 | Esophagus | ESCC | mRNA modification | 21/8552 | 27/18723 | 6.88e-04 | 3.61e-03 | 21 |
| 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:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
| GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
| 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 |
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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 |
| TRMT61A | SNV | Missense_Mutation | novel | c.551C>T | p.Ser184Leu | p.S184L | Q96FX7 | protein_coding | tolerated(0.55) | possibly_damaging(0.506) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRMT61A | SNV | Missense_Mutation | novel | c.94N>T | p.Arg32Cys | p.R32C | Q96FX7 | protein_coding | deleterious(0.02) | possibly_damaging(0.892) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TRMT61A | SNV | Missense_Mutation | rs781229023 | c.731G>T | p.Ser244Ile | p.S244I | Q96FX7 | protein_coding | tolerated(0.3) | benign(0.048) | TCGA-A6-6137-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | fluorouracil | SD |
| TRMT61A | SNV | Missense_Mutation | c.358G>A | p.Ala120Thr | p.A120T | Q96FX7 | protein_coding | deleterious(0.01) | probably_damaging(0.957) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRMT61A | SNV | Missense_Mutation | rs773491301 | c.121N>A | p.Gly41Ser | p.G41S | Q96FX7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD |
| TRMT61A | SNV | Missense_Mutation | rs781229023 | c.731N>T | p.Ser244Ile | p.S244I | Q96FX7 | protein_coding | tolerated(0.3) | benign(0.048) | TCGA-CM-6172-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Ancillary | leucovorin | SD |
| TRMT61A | SNV | Missense_Mutation | novel | c.722N>A | p.Arg241His | p.R241H | Q96FX7 | protein_coding | deleterious(0.04) | possibly_damaging(0.817) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| TRMT61A | SNV | Missense_Mutation | rs778902763 | c.398N>T | p.Thr133Met | p.T133M | Q96FX7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| TRMT61A | SNV | Missense_Mutation | novel | c.739N>T | p.Pro247Ser | p.P247S | Q96FX7 | protein_coding | tolerated(0.7) | benign(0) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| TRMT61A | SNV | Missense_Mutation | novel | c.119A>G | p.His40Arg | p.H40R | Q96FX7 | protein_coding | deleterious(0.01) | possibly_damaging(0.53) | TCGA-BG-A220-01 | 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 |
| Page: 1 |
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