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Gene: MTMR4 |
Gene summary for MTMR4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MTMR4 | Gene ID | 9110 |
| Gene name | myotubularin related protein 4 | |
| Gene Alias | FYVE-DSP2 | |
| Cytomap | 17q22 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q9NYA4 |
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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 |
| 9110 | MTMR4 | LZE4T | Human | Esophagus | ESCC | 9.13e-05 | 1.97e-01 | 0.0811 |
| 9110 | MTMR4 | LZE7T | Human | Esophagus | ESCC | 6.29e-03 | 2.14e-01 | 0.0667 |
| 9110 | MTMR4 | LZE24T | Human | Esophagus | ESCC | 3.88e-06 | 2.24e-01 | 0.0596 |
| 9110 | MTMR4 | LZE21T | Human | Esophagus | ESCC | 8.50e-03 | 2.87e-01 | 0.0655 |
| 9110 | MTMR4 | P1T-E | Human | Esophagus | ESCC | 5.18e-08 | 3.47e-01 | 0.0875 |
| 9110 | MTMR4 | P2T-E | Human | Esophagus | ESCC | 1.03e-25 | 2.67e-01 | 0.1177 |
| 9110 | MTMR4 | P4T-E | Human | Esophagus | ESCC | 8.37e-09 | 2.00e-01 | 0.1323 |
| 9110 | MTMR4 | P8T-E | Human | Esophagus | ESCC | 6.84e-10 | 1.61e-01 | 0.0889 |
| 9110 | MTMR4 | P9T-E | Human | Esophagus | ESCC | 4.30e-10 | 1.28e-01 | 0.1131 |
| 9110 | MTMR4 | P10T-E | Human | Esophagus | ESCC | 2.01e-20 | 3.75e-01 | 0.116 |
| 9110 | MTMR4 | P11T-E | Human | Esophagus | ESCC | 5.45e-03 | 1.58e-01 | 0.1426 |
| 9110 | MTMR4 | P12T-E | Human | Esophagus | ESCC | 4.39e-22 | 2.72e-01 | 0.1122 |
| 9110 | MTMR4 | P15T-E | Human | Esophagus | ESCC | 1.24e-11 | 2.65e-01 | 0.1149 |
| 9110 | MTMR4 | P16T-E | Human | Esophagus | ESCC | 3.47e-11 | 2.35e-01 | 0.1153 |
| 9110 | MTMR4 | P17T-E | Human | Esophagus | ESCC | 2.77e-03 | 1.39e-01 | 0.1278 |
| 9110 | MTMR4 | P20T-E | Human | Esophagus | ESCC | 5.87e-04 | 1.05e-01 | 0.1124 |
| 9110 | MTMR4 | P21T-E | Human | Esophagus | ESCC | 4.10e-12 | 1.51e-01 | 0.1617 |
| 9110 | MTMR4 | P22T-E | Human | Esophagus | ESCC | 8.21e-09 | 2.30e-01 | 0.1236 |
| 9110 | MTMR4 | P23T-E | Human | Esophagus | ESCC | 1.36e-14 | 3.47e-01 | 0.108 |
| 9110 | MTMR4 | P24T-E | Human | Esophagus | ESCC | 3.65e-10 | 1.66e-01 | 0.1287 |
| 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 | ||
| 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:001050617 | Esophagus | ESCC | regulation of autophagy | 220/8552 | 317/18723 | 6.72e-18 | 6.36e-16 | 220 |
| GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:0035303111 | Esophagus | ESCC | regulation of dephosphorylation | 88/8552 | 128/18723 | 1.04e-07 | 1.71e-06 | 88 |
| GO:00715599 | Esophagus | ESCC | response to transforming growth factor beta | 157/8552 | 256/18723 | 2.95e-07 | 4.23e-06 | 157 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:00715609 | Esophagus | ESCC | cellular response to transforming growth factor beta stimulus | 151/8552 | 250/18723 | 1.78e-06 | 2.10e-05 | 151 |
| GO:00066446 | Esophagus | ESCC | phospholipid metabolic process | 218/8552 | 383/18723 | 5.37e-06 | 5.59e-05 | 218 |
| GO:00071799 | Esophagus | ESCC | transforming growth factor beta receptor signaling pathway | 121/8552 | 198/18723 | 8.26e-06 | 8.03e-05 | 121 |
| GO:00066505 | Esophagus | ESCC | glycerophospholipid metabolic process | 174/8552 | 306/18723 | 4.92e-05 | 3.85e-04 | 174 |
| GO:000717810 | Esophagus | ESCC | transmembrane receptor protein serine/threonine kinase signaling pathway | 195/8552 | 355/18723 | 2.58e-04 | 1.58e-03 | 195 |
| GO:00464864 | Esophagus | ESCC | glycerolipid metabolic process | 211/8552 | 392/18723 | 6.51e-04 | 3.46e-03 | 211 |
| GO:00170156 | Esophagus | ESCC | regulation of transforming growth factor beta receptor signaling pathway | 75/8552 | 128/18723 | 2.19e-03 | 9.71e-03 | 75 |
| GO:19038447 | Esophagus | ESCC | regulation of cellular response to transforming growth factor beta stimulus | 76/8552 | 131/18723 | 2.96e-03 | 1.24e-02 | 76 |
| GO:00302586 | Esophagus | ESCC | lipid modification | 116/8552 | 212/18723 | 4.90e-03 | 1.89e-02 | 116 |
| GO:00192168 | Esophagus | ESCC | regulation of lipid metabolic process | 172/8552 | 331/18723 | 1.20e-02 | 4.02e-02 | 172 |
| GO:00066611 | Esophagus | ESCC | phosphatidylinositol biosynthetic process | 73/8552 | 131/18723 | 1.31e-02 | 4.28e-02 | 73 |
| GO:00302585 | Liver | NAFLD | lipid modification | 49/1882 | 212/18723 | 1.97e-08 | 2.17e-06 | 49 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0414021 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
| hsa0414031 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
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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 |
| MTMR4 | SNV | Missense_Mutation | c.1730G>A | p.Cys577Tyr | p.C577Y | Q9NYA4 | protein_coding | deleterious(0.01) | benign(0.374) | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| MTMR4 | SNV | Missense_Mutation | novel | c.3304N>T | p.Asp1102Tyr | p.D1102Y | Q9NYA4 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MTMR4 | SNV | Missense_Mutation | c.2899N>G | p.His967Asp | p.H967D | Q9NYA4 | protein_coding | tolerated_low_confidence(0.34) | benign(0.072) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| MTMR4 | SNV | Missense_Mutation | c.2278N>T | p.Ala760Ser | p.A760S | Q9NYA4 | protein_coding | tolerated_low_confidence(0.92) | benign(0) | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | |
| MTMR4 | SNV | Missense_Mutation | rs745483455 | c.1546N>C | p.Cys516Arg | p.C516R | Q9NYA4 | protein_coding | tolerated(0.74) | benign(0.001) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| MTMR4 | SNV | Missense_Mutation | c.1738N>C | p.Gly580Arg | p.G580R | Q9NYA4 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-BH-A0HI-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| MTMR4 | SNV | Missense_Mutation | novel | c.3400N>T | p.His1134Tyr | p.H1134Y | Q9NYA4 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E2-A15R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| MTMR4 | insertion | Frame_Shift_Ins | novel | c.455-1_455insACACTTGCGCAATGGGGCTGCCATCGCCCGCT | p.Gly152AspfsTer151 | p.G152Dfs*151 | Q9NYA4 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| MTMR4 | insertion | In_Frame_Ins | novel | c.714_715insTGTTGCCCAGGCTGGACTGCAGTGGCACAATCT | p.Ile238_Ser239insCysCysProGlyTrpThrAlaValAlaGlnSer | p.I238_S239insCCPGWTAVAQS | Q9NYA4 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| MTMR4 | insertion | In_Frame_Ins | novel | c.938_939insAGGGAAATGGGT | p.Ser313_Tyr314insGlyLysTrpVal | p.S313_Y314insGKWV | Q9NYA4 | protein_coding | TCGA-BH-A0BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
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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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