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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: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:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
GO:000640121 | Liver | HCC | RNA catabolic process | 201/7958 | 278/18723 | 3.88e-24 | 1.02e-21 | 201 |
GO:003465521 | Liver | HCC | nucleobase-containing compound catabolic process | 273/7958 | 407/18723 | 4.84e-24 | 1.23e-21 | 273 |
GO:004348721 | Liver | HCC | regulation of RNA stability | 119/7958 | 170/18723 | 3.20e-13 | 1.71e-11 | 119 |
GO:000989522 | Liver | HCC | negative regulation of catabolic process | 196/7958 | 320/18723 | 7.98e-12 | 3.35e-10 | 196 |
GO:003133022 | Liver | HCC | negative regulation of cellular catabolic process | 164/7958 | 262/18723 | 3.52e-11 | 1.35e-09 | 164 |
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 |
GO:0001510 | Liver | HCC | RNA methylation | 53/7958 | 83/18723 | 6.96e-05 | 6.29e-04 | 53 |
GO:00346611 | Liver | HCC | ncRNA catabolic process | 31/7958 | 43/18723 | 8.13e-05 | 7.19e-04 | 31 |
GO:0030488 | Liver | HCC | tRNA methylation | 29/7958 | 41/18723 | 2.38e-04 | 1.79e-03 | 29 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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.713N>G | p.Ile238Ser | p.I238S | O14717 | protein_coding | tolerated(0.11) | benign(0.021) | TCGA-IN-7808-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | PD | |
TRDMT1 | SNV | Missense_Mutation | novel | c.936G>T | p.Glu312Asp | p.E312D | O14717 | protein_coding | tolerated(0.42) | benign(0.006) | TCGA-VQ-A94P-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | PD |
TRDMT1 | SNV | Missense_Mutation | c.1066N>T | p.Pro356Ser | p.P356S | O14717 | protein_coding | tolerated(0.22) | benign(0.001) | TCGA-VQ-A94T-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD | |
TRDMT1 | insertion | Frame_Shift_Ins | novel | c.715_716insTGGAT | p.His239LeufsTer14 | p.H239Lfs*14 | O14717 | protein_coding | TCGA-BR-8486-01 | Stomach | stomach adenocarcinoma | 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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