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Gene: MTM1 |
Gene summary for MTM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MTM1 | Gene ID | 4534 |
| Gene name | myotubularin 1 | |
| Gene Alias | CNM | |
| Cytomap | Xq28 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | A0A024RC06 |
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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 |
| 4534 | MTM1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.90e-10 | -5.11e-01 | 0.0155 |
| 4534 | MTM1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.85e-12 | 6.65e-01 | -0.1954 |
| 4534 | MTM1 | HTA11_866_3004761011 | Human | Colorectum | AD | 7.96e-05 | -4.59e-01 | 0.096 |
| 4534 | MTM1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.02e-08 | -4.50e-01 | 0.0674 |
| 4534 | MTM1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 4.71e-12 | -4.87e-01 | 0.294 |
| 4534 | MTM1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.48e-02 | -3.82e-01 | 0.3859 |
| 4534 | MTM1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 5.98e-04 | -6.12e-01 | 0.2585 |
| 4534 | MTM1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.05e-09 | -4.52e-01 | 0.3005 |
| 4534 | MTM1 | F007 | Human | Colorectum | FAP | 5.83e-04 | -4.29e-01 | 0.1176 |
| 4534 | MTM1 | A001-C-207 | Human | Colorectum | FAP | 2.43e-07 | -4.33e-01 | 0.1278 |
| 4534 | MTM1 | A015-C-203 | Human | Colorectum | FAP | 3.26e-28 | -5.84e-01 | -0.1294 |
| 4534 | MTM1 | A015-C-204 | Human | Colorectum | FAP | 1.15e-13 | -5.93e-01 | -0.0228 |
| 4534 | MTM1 | A014-C-040 | Human | Colorectum | FAP | 1.86e-02 | -3.08e-01 | -0.1184 |
| 4534 | MTM1 | A002-C-201 | Human | Colorectum | FAP | 1.30e-16 | -4.96e-01 | 0.0324 |
| 4534 | MTM1 | A002-C-203 | Human | Colorectum | FAP | 2.89e-04 | -3.37e-01 | 0.2786 |
| 4534 | MTM1 | A001-C-119 | Human | Colorectum | FAP | 4.63e-11 | -5.95e-01 | -0.1557 |
| 4534 | MTM1 | A001-C-108 | Human | Colorectum | FAP | 1.96e-19 | -5.11e-01 | -0.0272 |
| 4534 | MTM1 | A002-C-205 | Human | Colorectum | FAP | 1.32e-23 | -5.93e-01 | -0.1236 |
| 4534 | MTM1 | A001-C-104 | Human | Colorectum | FAP | 1.13e-05 | -4.02e-01 | 0.0184 |
| 4534 | MTM1 | A015-C-005 | Human | Colorectum | FAP | 4.32e-12 | -5.30e-01 | -0.0336 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
| GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0010639 | Colorectum | AD | negative regulation of organelle organization | 114/3918 | 348/18723 | 1.41e-07 | 6.49e-06 | 114 |
| GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
| GO:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0006470 | Colorectum | AD | protein dephosphorylation | 88/3918 | 281/18723 | 2.56e-05 | 4.89e-04 | 88 |
| GO:0016241 | Colorectum | AD | regulation of macroautophagy | 50/3918 | 141/18723 | 4.55e-05 | 7.92e-04 | 50 |
| GO:0007041 | Colorectum | AD | lysosomal transport | 42/3918 | 114/18723 | 6.61e-05 | 1.07e-03 | 42 |
| GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
| GO:0030258 | Colorectum | AD | lipid modification | 67/3918 | 212/18723 | 1.66e-04 | 2.27e-03 | 67 |
| GO:0070584 | Colorectum | AD | mitochondrion morphogenesis | 12/3918 | 21/18723 | 3.02e-04 | 3.62e-03 | 12 |
| GO:0010507 | Colorectum | AD | negative regulation of autophagy | 31/3918 | 85/18723 | 6.91e-04 | 7.05e-03 | 31 |
| GO:0007033 | Colorectum | AD | vacuole organization | 53/3918 | 180/18723 | 4.18e-03 | 2.89e-02 | 53 |
| GO:0006650 | Colorectum | AD | glycerophospholipid metabolic process | 83/3918 | 306/18723 | 5.40e-03 | 3.55e-02 | 83 |
| GO:0006644 | Colorectum | AD | phospholipid metabolic process | 101/3918 | 383/18723 | 5.80e-03 | 3.67e-02 | 101 |
| GO:0045017 | Colorectum | AD | glycerolipid biosynthetic process | 69/3918 | 252/18723 | 8.33e-03 | 4.88e-02 | 69 |
| GO:00313302 | Colorectum | MSS | negative regulation of cellular catabolic process | 96/3467 | 262/18723 | 2.67e-12 | 4.63e-10 | 96 |
| GO:00098952 | Colorectum | MSS | negative regulation of catabolic process | 110/3467 | 320/18723 | 7.88e-12 | 1.20e-09 | 110 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04070 | Colorectum | CRC | Phosphatidylinositol signaling system | 25/1091 | 97/8465 | 4.27e-04 | 4.60e-03 | 3.12e-03 | 25 |
| hsa00562 | Colorectum | CRC | Inositol phosphate metabolism | 18/1091 | 73/8465 | 4.38e-03 | 2.52e-02 | 1.71e-02 | 18 |
| hsa040701 | Colorectum | CRC | Phosphatidylinositol signaling system | 25/1091 | 97/8465 | 4.27e-04 | 4.60e-03 | 3.12e-03 | 25 |
| hsa005621 | Colorectum | CRC | Inositol phosphate metabolism | 18/1091 | 73/8465 | 4.38e-03 | 2.52e-02 | 1.71e-02 | 18 |
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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 |
| MTM1 | SNV | Missense_Mutation | c.1344N>C | p.Met448Ile | p.M448I | Q13496 | protein_coding | tolerated(0.37) | benign(0.003) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD | |
| MTM1 | SNV | Missense_Mutation | c.365N>A | p.Ala122Asp | p.A122D | Q13496 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A7-A26G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| MTM1 | SNV | Missense_Mutation | c.1097N>T | p.Ser366Leu | p.S366L | Q13496 | protein_coding | deleterious(0.02) | benign(0.04) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| MTM1 | SNV | Missense_Mutation | rs781995404 | c.539A>G | p.Asn180Ser | p.N180S | Q13496 | protein_coding | tolerated(0.06) | benign(0.021) | TCGA-A8-A0AD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| MTM1 | SNV | Missense_Mutation | novel | c.859N>A | p.Ala287Thr | p.A287T | Q13496 | protein_coding | tolerated(0.26) | benign(0.154) | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MTM1 | SNV | Missense_Mutation | c.698N>T | p.Pro233Leu | p.P233L | Q13496 | protein_coding | deleterious(0.02) | possibly_damaging(0.73) | TCGA-B6-A0IH-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| MTM1 | SNV | Missense_Mutation | c.302N>T | p.Ser101Ile | p.S101I | Q13496 | protein_coding | deleterious(0) | possibly_damaging(0.772) | TCGA-D8-A1XF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| MTM1 | SNV | Missense_Mutation | c.1164G>C | p.Leu388Phe | p.L388F | Q13496 | protein_coding | deleterious(0.04) | probably_damaging(0.998) | TCGA-EW-A1PA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| MTM1 | SNV | Missense_Mutation | novel | c.1384T>C | p.Phe462Leu | p.F462L | Q13496 | protein_coding | tolerated(0.32) | benign(0.015) | TCGA-OL-A66J-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MTM1 | insertion | Nonsense_Mutation | c.418_419insCCATGGTCCAGCACAGCACTCCTTTATCTGAAATGAAAGTTTA | p.Tyr140SerfsTer15 | p.Y140Sfs*15 | Q13496 | protein_coding | TCGA-A8-A0A4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR |
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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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