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Gene: YTHDF1 |
Gene summary for YTHDF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YTHDF1 | Gene ID | 54915 |
| Gene name | YTH N6-methyladenosine RNA binding protein 1 | |
| Gene Alias | C20orf21 | |
| Cytomap | 20q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9BYJ9 |
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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 |
| 54915 | YTHDF1 | LZE20T | Human | Esophagus | ESCC | 1.22e-02 | -3.80e-03 | 0.0662 |
| 54915 | YTHDF1 | LZE24T | Human | Esophagus | ESCC | 4.46e-06 | 8.67e-02 | 0.0596 |
| 54915 | YTHDF1 | P2T-E | Human | Esophagus | ESCC | 9.88e-08 | 1.96e-02 | 0.1177 |
| 54915 | YTHDF1 | P4T-E | Human | Esophagus | ESCC | 1.52e-10 | 6.36e-02 | 0.1323 |
| 54915 | YTHDF1 | P5T-E | Human | Esophagus | ESCC | 4.51e-27 | 1.30e-01 | 0.1327 |
| 54915 | YTHDF1 | P8T-E | Human | Esophagus | ESCC | 6.18e-04 | -1.67e-03 | 0.0889 |
| 54915 | YTHDF1 | P9T-E | Human | Esophagus | ESCC | 8.67e-08 | 6.91e-02 | 0.1131 |
| 54915 | YTHDF1 | P10T-E | Human | Esophagus | ESCC | 9.55e-14 | 1.56e-01 | 0.116 |
| 54915 | YTHDF1 | P11T-E | Human | Esophagus | ESCC | 4.03e-03 | 2.56e-01 | 0.1426 |
| 54915 | YTHDF1 | P12T-E | Human | Esophagus | ESCC | 1.14e-20 | 1.70e-01 | 0.1122 |
| 54915 | YTHDF1 | P15T-E | Human | Esophagus | ESCC | 2.41e-06 | 1.59e-01 | 0.1149 |
| 54915 | YTHDF1 | P16T-E | Human | Esophagus | ESCC | 2.44e-11 | 8.21e-02 | 0.1153 |
| 54915 | YTHDF1 | P17T-E | Human | Esophagus | ESCC | 6.75e-06 | 2.41e-01 | 0.1278 |
| 54915 | YTHDF1 | P20T-E | Human | Esophagus | ESCC | 1.65e-13 | 1.51e-01 | 0.1124 |
| 54915 | YTHDF1 | P21T-E | Human | Esophagus | ESCC | 2.85e-15 | 1.03e-01 | 0.1617 |
| 54915 | YTHDF1 | P22T-E | Human | Esophagus | ESCC | 3.20e-12 | 1.64e-01 | 0.1236 |
| 54915 | YTHDF1 | P23T-E | Human | Esophagus | ESCC | 1.31e-14 | 2.98e-01 | 0.108 |
| 54915 | YTHDF1 | P24T-E | Human | Esophagus | ESCC | 2.83e-11 | 7.13e-02 | 0.1287 |
| 54915 | YTHDF1 | P26T-E | Human | Esophagus | ESCC | 1.14e-22 | 1.63e-01 | 0.1276 |
| 54915 | YTHDF1 | P27T-E | Human | Esophagus | ESCC | 2.71e-05 | -1.51e-02 | 0.1055 |
| 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:0009896111 | Esophagus | ESCC | positive regulation of catabolic process | 332/8552 | 492/18723 | 4.36e-23 | 9.22e-21 | 332 |
| GO:0031331111 | Esophagus | ESCC | positive regulation of cellular catabolic process | 292/8552 | 427/18723 | 8.67e-22 | 1.53e-19 | 292 |
| GO:1903311110 | Esophagus | ESCC | regulation of mRNA metabolic process | 210/8552 | 288/18723 | 3.25e-21 | 5.56e-19 | 210 |
| GO:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:0006413110 | Esophagus | ESCC | translational initiation | 100/8552 | 118/18723 | 1.16e-18 | 1.25e-16 | 100 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:0006402110 | Esophagus | ESCC | mRNA catabolic process | 170/8552 | 232/18723 | 8.70e-18 | 8.00e-16 | 170 |
| GO:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:0045727111 | Esophagus | ESCC | positive regulation of translation | 107/8552 | 136/18723 | 2.79e-15 | 1.68e-13 | 107 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:0034250111 | Esophagus | ESCC | positive regulation of cellular amide metabolic process | 123/8552 | 162/18723 | 3.32e-15 | 1.93e-13 | 123 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:000644617 | Esophagus | ESCC | regulation of translational initiation | 65/8552 | 79/18723 | 2.04e-11 | 7.07e-10 | 65 |
| GO:190331316 | Esophagus | ESCC | positive regulation of mRNA metabolic process | 87/8552 | 118/18723 | 5.10e-10 | 1.32e-08 | 87 |
| GO:006101319 | Esophagus | ESCC | regulation of mRNA catabolic process | 115/8552 | 166/18723 | 5.90e-10 | 1.49e-08 | 115 |
| GO:004348719 | Esophagus | ESCC | regulation of RNA stability | 117/8552 | 170/18723 | 7.91e-10 | 1.94e-08 | 117 |
| GO:004348819 | Esophagus | ESCC | regulation of mRNA stability | 109/8552 | 158/18723 | 2.40e-09 | 5.35e-08 | 109 |
| GO:006101416 | Esophagus | ESCC | positive regulation of mRNA catabolic process | 63/8552 | 87/18723 | 3.70e-07 | 5.15e-06 | 63 |
| Page: 1 2 3 4 5 6 |
| 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 |
| YTHDF1 | SNV | Missense_Mutation | c.75G>C | p.Gln25His | p.Q25H | Q9BYJ9 | protein_coding | deleterious(0.03) | probably_damaging(0.94) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| YTHDF1 | SNV | Missense_Mutation | novel | c.1399N>A | p.Gln467Lys | p.Q467K | Q9BYJ9 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| YTHDF1 | SNV | Missense_Mutation | c.385N>C | p.Phe129Leu | p.F129L | Q9BYJ9 | protein_coding | deleterious(0) | possibly_damaging(0.828) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| YTHDF1 | SNV | Missense_Mutation | c.737C>A | p.Pro246His | p.P246H | Q9BYJ9 | protein_coding | deleterious(0.04) | possibly_damaging(0.873) | TCGA-D8-A1XT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| YTHDF1 | SNV | Missense_Mutation | c.1351N>A | p.Glu451Lys | p.E451K | Q9BYJ9 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| YTHDF1 | SNV | Missense_Mutation | novel | c.431N>A | p.Ser144Asn | p.S144N | Q9BYJ9 | protein_coding | tolerated(0.13) | benign(0.011) | TCGA-D8-A3Z6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphane | SD |
| YTHDF1 | insertion | Frame_Shift_Ins | novel | c.486_487insCCGAAGG | p.Val163ProfsTer4 | p.V163Pfs*4 | Q9BYJ9 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| YTHDF1 | insertion | In_Frame_Ins | novel | c.484_485insACATTGGCACCTGGGATAACAAGGGGCCTG | p.Thr161_Val162insAspIleGlyThrTrpAspAsnLysGlyPro | p.T161_V162insDIGTWDNKGP | Q9BYJ9 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| YTHDF1 | insertion | In_Frame_Ins | novel | c.1408_1409insCCTGGGTTGATACATTTTTTGGTTTTA | p.Trp470delinsSerTrpValAspThrPhePheGlyPheArg | p.W470delinsSWVDTFFGFR | Q9BYJ9 | protein_coding | TCGA-A8-A09D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | ||
| YTHDF1 | insertion | Frame_Shift_Ins | novel | c.1400_1401insCTTTCTCCTCTCCTTTTTGAATTGTGATACTTTCTGGAAC | p.Gln467HisfsTer22 | p.Q467Hfs*22 | Q9BYJ9 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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