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Gene: TRDMT1 |
Gene summary for TRDMT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRDMT1 | Gene ID | 1787 |
| Gene name | tRNA aspartic acid methyltransferase 1 | |
| Gene Alias | DMNT2 | |
| Cytomap | 10p13 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | B4DQZ2 |
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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 |
| 1787 | TRDMT1 | HCC1_Meng | Human | Liver | HCC | 3.31e-10 | -1.51e-02 | 0.0246 |
| 1787 | TRDMT1 | HCC1 | Human | Liver | HCC | 1.17e-09 | 8.84e-01 | 0.5336 |
| 1787 | TRDMT1 | HCC2 | Human | Liver | HCC | 1.38e-27 | 2.44e+00 | 0.5341 |
| 1787 | TRDMT1 | HCC5 | Human | Liver | HCC | 7.21e-35 | 1.78e+00 | 0.4932 |
| 1787 | TRDMT1 | S015 | Human | Liver | HCC | 8.59e-07 | 3.48e-01 | 0.2375 |
| 1787 | TRDMT1 | S016 | Human | Liver | HCC | 2.42e-03 | 1.92e-01 | 0.2243 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:190236921 | Liver | HCC | negative regulation of RNA catabolic process | 45/7958 | 75/18723 | 1.67e-03 | 8.73e-03 | 45 |
| GO:004348921 | Liver | HCC | RNA stabilization | 39/7958 | 65/18723 | 3.31e-03 | 1.51e-02 | 39 |
| GO:0016078 | Liver | HCC | tRNA catabolic process | 10/7958 | 13/18723 | 1.28e-02 | 4.61e-02 | 10 |
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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 |
| TRDMT1 | SNV | Missense_Mutation | c.604N>C | p.Glu202Gln | p.E202Q | O14717 | protein_coding | tolerated(0.25) | benign(0.011) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRDMT1 | SNV | Missense_Mutation | c.383N>T | p.Ser128Phe | p.S128F | O14717 | protein_coding | deleterious(0) | benign(0.41) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRDMT1 | insertion | Nonsense_Mutation | novel | c.959_960insATGAAAGGGGGACTCAGAAGATGAAATTGACACAGG | p.Tyr320delinsTer | p.Y320delins* | O14717 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TRDMT1 | SNV | Missense_Mutation | rs769202322 | c.1045G>A | p.Ala349Thr | p.A349T | O14717 | protein_coding | deleterious(0) | possibly_damaging(0.74) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TRDMT1 | SNV | Missense_Mutation | rs141411248 | c.512N>T | p.Ser171Leu | p.S171L | O14717 | protein_coding | tolerated(0.14) | benign(0.007) | TCGA-VS-A950-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| TRDMT1 | SNV | Missense_Mutation | rs776907517 | c.349N>A | p.Leu117Ile | p.L117I | O14717 | protein_coding | deleterious(0.01) | possibly_damaging(0.871) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRDMT1 | SNV | Missense_Mutation | c.216N>T | p.Met72Ile | p.M72I | O14717 | protein_coding | tolerated(0.19) | benign(0.006) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| TRDMT1 | SNV | Missense_Mutation | c.791N>G | p.Asn264Ser | p.N264S | O14717 | protein_coding | tolerated(1) | benign(0) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
| TRDMT1 | SNV | Missense_Mutation | rs371526424 | c.211N>A | p.Asp71Asn | p.D71N | O14717 | protein_coding | tolerated(0.33) | benign(0.023) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TRDMT1 | SNV | Missense_Mutation | c.1112N>A | p.Arg371His | p.R371H | O14717 | protein_coding | deleterious(0.01) | probably_damaging(0.926) | TCGA-AG-A02N-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | folinic | CR |
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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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