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Gene: YTHDF3 |
Gene summary for YTHDF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YTHDF3 | Gene ID | 253943 |
| Gene name | YTH N6-methyladenosine RNA binding protein 3 | |
| Gene Alias | DF3 | |
| Cytomap | 8q12.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A087WY31 |
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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 |
| 253943 | YTHDF3 | LZE4T | Human | Esophagus | ESCC | 4.34e-13 | 3.06e-01 | 0.0811 |
| 253943 | YTHDF3 | LZE5T | Human | Esophagus | ESCC | 4.35e-02 | 4.64e-02 | 0.0514 |
| 253943 | YTHDF3 | LZE8T | Human | Esophagus | ESCC | 1.85e-14 | 2.01e-01 | 0.067 |
| 253943 | YTHDF3 | LZE20T | Human | Esophagus | ESCC | 1.01e-05 | 2.04e-01 | 0.0662 |
| 253943 | YTHDF3 | LZE24T | Human | Esophagus | ESCC | 1.21e-13 | 3.74e-01 | 0.0596 |
| 253943 | YTHDF3 | LZE21T | Human | Esophagus | ESCC | 3.41e-03 | 2.53e-01 | 0.0655 |
| 253943 | YTHDF3 | P1T-E | Human | Esophagus | ESCC | 2.63e-05 | 1.72e-01 | 0.0875 |
| 253943 | YTHDF3 | P2T-E | Human | Esophagus | ESCC | 3.51e-10 | 2.45e-01 | 0.1177 |
| 253943 | YTHDF3 | P4T-E | Human | Esophagus | ESCC | 1.97e-13 | 2.50e-01 | 0.1323 |
| 253943 | YTHDF3 | P5T-E | Human | Esophagus | ESCC | 6.99e-14 | 2.06e-01 | 0.1327 |
| 253943 | YTHDF3 | P8T-E | Human | Esophagus | ESCC | 8.44e-15 | 2.21e-01 | 0.0889 |
| 253943 | YTHDF3 | P9T-E | Human | Esophagus | ESCC | 5.23e-11 | 1.26e-01 | 0.1131 |
| 253943 | YTHDF3 | P10T-E | Human | Esophagus | ESCC | 1.27e-17 | 3.21e-01 | 0.116 |
| 253943 | YTHDF3 | P11T-E | Human | Esophagus | ESCC | 2.09e-09 | 4.65e-01 | 0.1426 |
| 253943 | YTHDF3 | P12T-E | Human | Esophagus | ESCC | 2.72e-16 | 3.65e-01 | 0.1122 |
| 253943 | YTHDF3 | P15T-E | Human | Esophagus | ESCC | 1.22e-13 | 3.37e-01 | 0.1149 |
| 253943 | YTHDF3 | P16T-E | Human | Esophagus | ESCC | 5.30e-26 | 4.64e-01 | 0.1153 |
| 253943 | YTHDF3 | P17T-E | Human | Esophagus | ESCC | 2.73e-07 | 3.71e-01 | 0.1278 |
| 253943 | YTHDF3 | P20T-E | Human | Esophagus | ESCC | 1.07e-12 | 1.32e-01 | 0.1124 |
| 253943 | YTHDF3 | P21T-E | Human | Esophagus | ESCC | 2.56e-20 | 4.15e-01 | 0.1617 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:0009896210 | Thyroid | ATC | positive regulation of catabolic process | 290/6293 | 492/18723 | 2.15e-31 | 1.94e-28 | 290 |
| GO:0031331210 | Thyroid | ATC | positive regulation of cellular catabolic process | 258/6293 | 427/18723 | 2.09e-30 | 1.65e-27 | 258 |
| GO:190331134 | Thyroid | ATC | regulation of mRNA metabolic process | 181/6293 | 288/18723 | 1.75e-24 | 5.54e-22 | 181 |
| GO:000640127 | Thyroid | ATC | RNA catabolic process | 165/6293 | 278/18723 | 8.45e-19 | 1.14e-16 | 165 |
| GO:000640227 | Thyroid | ATC | mRNA catabolic process | 140/6293 | 232/18723 | 5.08e-17 | 4.65e-15 | 140 |
| GO:003465525 | Thyroid | ATC | nucleobase-containing compound catabolic process | 217/6293 | 407/18723 | 1.20e-16 | 1.04e-14 | 217 |
| GO:000641334 | Thyroid | ATC | translational initiation | 83/6293 | 118/18723 | 3.44e-16 | 2.88e-14 | 83 |
| GO:004670024 | Thyroid | ATC | heterocycle catabolic process | 228/6293 | 445/18723 | 7.26e-15 | 4.50e-13 | 228 |
| GO:004427025 | Thyroid | ATC | cellular nitrogen compound catabolic process | 229/6293 | 451/18723 | 2.25e-14 | 1.27e-12 | 229 |
| GO:000641735 | Thyroid | ATC | regulation of translation | 236/6293 | 468/18723 | 2.39e-14 | 1.34e-12 | 236 |
| GO:001943924 | Thyroid | ATC | aromatic compound catabolic process | 232/6293 | 467/18723 | 3.05e-13 | 1.44e-11 | 232 |
| GO:004572733 | Thyroid | ATC | positive regulation of translation | 85/6293 | 136/18723 | 4.71e-12 | 1.84e-10 | 85 |
| GO:003425034 | Thyroid | ATC | positive regulation of cellular amide metabolic process | 97/6293 | 162/18723 | 5.97e-12 | 2.30e-10 | 97 |
| GO:190136124 | Thyroid | ATC | organic cyclic compound catabolic process | 238/6293 | 495/18723 | 1.12e-11 | 4.12e-10 | 238 |
| GO:190331324 | Thyroid | ATC | positive regulation of mRNA metabolic process | 75/6293 | 118/18723 | 2.57e-11 | 8.84e-10 | 75 |
| GO:000166731 | Thyroid | ATC | ameboidal-type cell migration | 228/6293 | 475/18723 | 3.72e-11 | 1.22e-09 | 228 |
| GO:000644632 | Thyroid | ATC | regulation of translational initiation | 55/6293 | 79/18723 | 6.38e-11 | 2.06e-09 | 55 |
| GO:004348725 | Thyroid | ATC | regulation of RNA stability | 97/6293 | 170/18723 | 2.68e-10 | 7.70e-09 | 97 |
| GO:006101325 | Thyroid | ATC | regulation of mRNA catabolic process | 95/6293 | 166/18723 | 3.27e-10 | 9.16e-09 | 95 |
| GO:004348826 | Thyroid | ATC | regulation of mRNA stability | 90/6293 | 158/18723 | 1.31e-09 | 3.30e-08 | 90 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| 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 |
| YTHDF3 | SNV | Missense_Mutation | c.1320N>G | p.Ile440Met | p.I440M | protein_coding | deleterious(0) | benign(0.354) | TCGA-A8-A075-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | epirubicin | CR | ||
| YTHDF3 | SNV | Missense_Mutation | c.1351N>A | p.Leu451Met | p.L451M | protein_coding | deleterious(0) | possibly_damaging(0.775) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| YTHDF3 | SNV | Missense_Mutation | c.706C>T | p.Pro236Ser | p.P236S | protein_coding | tolerated(0.24) | probably_damaging(0.954) | TCGA-B6-A0I8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| YTHDF3 | SNV | Missense_Mutation | c.1429N>G | p.Cys477Gly | p.C477G | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-B6-A0RS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| YTHDF3 | SNV | Missense_Mutation | novel | c.172N>T | p.Pro58Ser | p.P58S | protein_coding | tolerated(0.71) | benign(0.094) | TCGA-LL-A740-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
| YTHDF3 | insertion | Nonsense_Mutation | novel | c.348_349insTTCTTATGACATGATTAGATATGCAT | p.Asn117PhefsTer3 | p.N117Ffs*3 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| YTHDF3 | insertion | Nonsense_Mutation | novel | c.350_351insATTATACTTTTAGAAAAT | p.Asn117delinsLysLeuTyrPheTerLysIle | p.N117delinsKLYF*KI | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| YTHDF3 | insertion | Frame_Shift_Ins | novel | c.1316_1317insT | p.Ile440TyrfsTer4 | p.I440Yfs*4 | protein_coding | TCGA-D8-A73U-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| YTHDF3 | SNV | Missense_Mutation | rs767444673 | c.1568N>A | p.Arg523His | p.R523H | protein_coding | deleterious(0.02) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| YTHDF3 | SNV | Missense_Mutation | rs372046184 | c.1469N>T | p.Ala490Val | p.A490V | protein_coding | deleterious(0.01) | benign(0.41) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 |
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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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