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Gene: TYW5 |
Gene summary for TYW5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TYW5 | Gene ID | 129450 |
| Gene name | tRNA-yW synthesizing protein 5 | |
| Gene Alias | C2orf60 | |
| Cytomap | 2q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | A2RUC4 |
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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 |
| 129450 | TYW5 | LZE4T | Human | Esophagus | ESCC | 4.34e-02 | 1.12e-01 | 0.0811 |
| 129450 | TYW5 | LZE7T | Human | Esophagus | ESCC | 2.97e-03 | 1.94e-01 | 0.0667 |
| 129450 | TYW5 | LZE24T | Human | Esophagus | ESCC | 6.91e-09 | 1.79e-01 | 0.0596 |
| 129450 | TYW5 | P2T-E | Human | Esophagus | ESCC | 4.16e-05 | 1.30e-01 | 0.1177 |
| 129450 | TYW5 | P4T-E | Human | Esophagus | ESCC | 7.92e-14 | 3.67e-01 | 0.1323 |
| 129450 | TYW5 | P5T-E | Human | Esophagus | ESCC | 1.08e-05 | 1.68e-01 | 0.1327 |
| 129450 | TYW5 | P8T-E | Human | Esophagus | ESCC | 8.65e-04 | 9.80e-02 | 0.0889 |
| 129450 | TYW5 | P10T-E | Human | Esophagus | ESCC | 1.20e-05 | 1.37e-01 | 0.116 |
| 129450 | TYW5 | P11T-E | Human | Esophagus | ESCC | 9.76e-05 | 1.58e-01 | 0.1426 |
| 129450 | TYW5 | P12T-E | Human | Esophagus | ESCC | 1.89e-10 | 2.58e-01 | 0.1122 |
| 129450 | TYW5 | P15T-E | Human | Esophagus | ESCC | 4.37e-13 | 2.44e-01 | 0.1149 |
| 129450 | TYW5 | P16T-E | Human | Esophagus | ESCC | 1.91e-11 | 2.14e-01 | 0.1153 |
| 129450 | TYW5 | P17T-E | Human | Esophagus | ESCC | 6.81e-04 | 1.55e-01 | 0.1278 |
| 129450 | TYW5 | P20T-E | Human | Esophagus | ESCC | 4.58e-07 | 1.46e-01 | 0.1124 |
| 129450 | TYW5 | P21T-E | Human | Esophagus | ESCC | 8.32e-07 | 1.56e-01 | 0.1617 |
| 129450 | TYW5 | P22T-E | Human | Esophagus | ESCC | 1.51e-14 | 1.50e-01 | 0.1236 |
| 129450 | TYW5 | P23T-E | Human | Esophagus | ESCC | 2.46e-08 | 1.22e-01 | 0.108 |
| 129450 | TYW5 | P24T-E | Human | Esophagus | ESCC | 7.44e-08 | 1.53e-01 | 0.1287 |
| 129450 | TYW5 | P26T-E | Human | Esophagus | ESCC | 1.56e-06 | 1.54e-01 | 0.1276 |
| 129450 | TYW5 | P27T-E | Human | Esophagus | ESCC | 1.10e-08 | 1.76e-01 | 0.1055 |
| Page: 1 2 3 4 |
| 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 |
| ∗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: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:19016574 | Esophagus | ESCC | glycosyl compound metabolic process | 57/8552 | 88/18723 | 2.32e-04 | 1.44e-03 | 57 |
| 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:19016571 | Liver | HCC | glycosyl compound metabolic process | 55/7958 | 88/18723 | 1.20e-04 | 1.01e-03 | 55 |
| Page: 1 |
| 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 |
| TYW5 | SNV | Missense_Mutation | c.511N>A | p.Val171Met | p.V171M | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AA-3509-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TYW5 | SNV | Missense_Mutation | rs760126102 | c.322C>T | p.Arg108Trp | p.R108W | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TYW5 | SNV | Missense_Mutation | rs760126102 | c.322N>T | p.Arg108Trp | p.R108W | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TYW5 | SNV | Missense_Mutation | novel | c.697N>C | p.Trp233Arg | p.W233R | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TYW5 | SNV | Missense_Mutation | c.899N>A | p.Arg300Gln | p.R300Q | A2RUC4 | protein_coding | tolerated(0.14) | benign(0.001) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| TYW5 | SNV | Missense_Mutation | novel | c.263N>T | p.Arg88Met | p.R88M | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TYW5 | SNV | Missense_Mutation | novel | c.233N>T | p.Arg78Ile | p.R78I | A2RUC4 | protein_coding | deleterious(0) | possibly_damaging(0.744) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TYW5 | SNV | Missense_Mutation | c.682N>C | p.Phe228Leu | p.F228L | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A5-A0GV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TYW5 | SNV | Missense_Mutation | novel | c.814G>A | p.Ala272Thr | p.A272T | A2RUC4 | protein_coding | deleterious(0) | probably_damaging(0.925) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TYW5 | SNV | Missense_Mutation | novel | c.191N>T | p.Ala64Val | p.A64V | A2RUC4 | protein_coding | tolerated(0.23) | benign(0.012) | TCGA-AP-A1DO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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