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Gene: POMT2 |
Gene summary for POMT2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | POMT2 | Gene ID | 29954 |
| Gene name | protein O-mannosyltransferase 2 | |
| Gene Alias | LGMD2N | |
| Cytomap | 14q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q9UKY4 |
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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 |
| 29954 | POMT2 | LZE22T | Human | Esophagus | ESCC | 7.51e-04 | 2.38e-01 | 0.068 |
| 29954 | POMT2 | LZE24T | Human | Esophagus | ESCC | 4.84e-08 | 1.71e-01 | 0.0596 |
| 29954 | POMT2 | P2T-E | Human | Esophagus | ESCC | 5.73e-11 | 1.23e-01 | 0.1177 |
| 29954 | POMT2 | P4T-E | Human | Esophagus | ESCC | 4.52e-08 | 1.43e-01 | 0.1323 |
| 29954 | POMT2 | P5T-E | Human | Esophagus | ESCC | 8.80e-03 | 7.33e-02 | 0.1327 |
| 29954 | POMT2 | P8T-E | Human | Esophagus | ESCC | 8.60e-06 | 1.31e-01 | 0.0889 |
| 29954 | POMT2 | P9T-E | Human | Esophagus | ESCC | 6.71e-06 | 1.22e-01 | 0.1131 |
| 29954 | POMT2 | P10T-E | Human | Esophagus | ESCC | 3.32e-16 | 3.26e-01 | 0.116 |
| 29954 | POMT2 | P11T-E | Human | Esophagus | ESCC | 4.50e-09 | 3.49e-01 | 0.1426 |
| 29954 | POMT2 | P12T-E | Human | Esophagus | ESCC | 4.10e-15 | 2.56e-01 | 0.1122 |
| 29954 | POMT2 | P15T-E | Human | Esophagus | ESCC | 1.94e-09 | 2.06e-01 | 0.1149 |
| 29954 | POMT2 | P16T-E | Human | Esophagus | ESCC | 1.92e-10 | 1.33e-01 | 0.1153 |
| 29954 | POMT2 | P17T-E | Human | Esophagus | ESCC | 7.26e-03 | 2.40e-01 | 0.1278 |
| 29954 | POMT2 | P20T-E | Human | Esophagus | ESCC | 1.34e-10 | 1.33e-01 | 0.1124 |
| 29954 | POMT2 | P21T-E | Human | Esophagus | ESCC | 7.53e-08 | 1.18e-01 | 0.1617 |
| 29954 | POMT2 | P22T-E | Human | Esophagus | ESCC | 3.88e-09 | 1.48e-01 | 0.1236 |
| 29954 | POMT2 | P23T-E | Human | Esophagus | ESCC | 2.26e-09 | 1.35e-01 | 0.108 |
| 29954 | POMT2 | P24T-E | Human | Esophagus | ESCC | 6.19e-07 | 1.56e-01 | 0.1287 |
| 29954 | POMT2 | P26T-E | Human | Esophagus | ESCC | 2.79e-15 | 2.44e-01 | 0.1276 |
| 29954 | POMT2 | P27T-E | Human | Esophagus | ESCC | 4.45e-11 | 2.24e-01 | 0.1055 |
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| 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 |
| ∗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:00091002 | Esophagus | ESCC | glycoprotein metabolic process | 226/8552 | 387/18723 | 2.64e-07 | 3.94e-06 | 226 |
| GO:00700854 | Esophagus | ESCC | glycosylation | 144/8552 | 240/18723 | 5.12e-06 | 5.38e-05 | 144 |
| GO:00064865 | Esophagus | ESCC | protein glycosylation | 135/8552 | 226/18723 | 1.36e-05 | 1.24e-04 | 135 |
| GO:00434135 | Esophagus | ESCC | macromolecule glycosylation | 135/8552 | 226/18723 | 1.36e-05 | 1.24e-04 | 135 |
| GO:00091012 | Esophagus | ESCC | glycoprotein biosynthetic process | 181/8552 | 317/18723 | 2.54e-05 | 2.15e-04 | 181 |
| GO:00064931 | Esophagus | ESCC | protein O-linked glycosylation | 51/8552 | 86/18723 | 7.54e-03 | 2.70e-02 | 51 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| POMT2 | SNV | Missense_Mutation | novel | c.1070C>T | p.Ser357Phe | p.S357F | Q9UKY4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A4S1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| POMT2 | SNV | Missense_Mutation | c.609N>G | p.Ile203Met | p.I203M | Q9UKY4 | protein_coding | tolerated(0.38) | benign(0.257) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| POMT2 | SNV | Missense_Mutation | c.700N>T | p.Val234Phe | p.V234F | Q9UKY4 | protein_coding | tolerated(0.08) | possibly_damaging(0.519) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| POMT2 | SNV | Missense_Mutation | c.721N>A | p.Gly241Arg | p.G241R | Q9UKY4 | protein_coding | tolerated(0.08) | probably_damaging(0.954) | TCGA-BH-A28Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| POMT2 | SNV | Missense_Mutation | c.719N>C | p.Leu240Ser | p.L240S | Q9UKY4 | protein_coding | deleterious(0) | benign(0.219) | TCGA-D8-A1XC-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| POMT2 | insertion | Frame_Shift_Ins | novel | c.376_377insAATGCAGAAGT | p.Thr126LysfsTer23 | p.T126Kfs*23 | Q9UKY4 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| POMT2 | insertion | Nonsense_Mutation | novel | c.825_826insCTATAGGGAGATGACATGGGTGGGAGAGTCGA | p.Gly276LeufsTer2 | p.G276Lfs*2 | Q9UKY4 | protein_coding | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | ||
| POMT2 | insertion | Nonsense_Mutation | novel | c.686_687insGGGACAGTAGAGGAAG | p.Ser230GlyfsTer3 | p.S230Gfs*3 | Q9UKY4 | protein_coding | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| POMT2 | deletion | Frame_Shift_Del | novel | c.1094delN | p.Gly365AlafsTer33 | p.G365Afs*33 | Q9UKY4 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| POMT2 | SNV | Missense_Mutation | rs746000047 | c.1423C>T | p.Arg475Cys | p.R475C | Q9UKY4 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | 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 |
| Page: 1 |
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