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Gene: TMEM53 |
Gene summary for TMEM53 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM53 | Gene ID | 79639 |
| Gene name | transmembrane protein 53 | |
| Gene Alias | NET4 | |
| Cytomap | 1p34.1 | |
| Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | Q6P2H8 |
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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 |
| 79639 | TMEM53 | P36T-E | Human | Esophagus | ESCC | 2.01e-02 | 9.39e-02 | 0.1187 |
| 79639 | TMEM53 | P37T-E | Human | Esophagus | ESCC | 5.89e-16 | 3.34e-01 | 0.1371 |
| 79639 | TMEM53 | P39T-E | Human | Esophagus | ESCC | 4.24e-18 | 3.19e-01 | 0.0894 |
| 79639 | TMEM53 | P40T-E | Human | Esophagus | ESCC | 1.19e-04 | 2.18e-01 | 0.109 |
| 79639 | TMEM53 | P42T-E | Human | Esophagus | ESCC | 1.87e-03 | 1.38e-01 | 0.1175 |
| 79639 | TMEM53 | P47T-E | Human | Esophagus | ESCC | 9.44e-07 | 1.44e-01 | 0.1067 |
| 79639 | TMEM53 | P48T-E | Human | Esophagus | ESCC | 9.44e-07 | 1.43e-01 | 0.0959 |
| 79639 | TMEM53 | P49T-E | Human | Esophagus | ESCC | 3.49e-03 | 4.21e-01 | 0.1768 |
| 79639 | TMEM53 | P52T-E | Human | Esophagus | ESCC | 2.03e-09 | 1.85e-01 | 0.1555 |
| 79639 | TMEM53 | P54T-E | Human | Esophagus | ESCC | 7.51e-22 | 4.86e-01 | 0.0975 |
| 79639 | TMEM53 | P57T-E | Human | Esophagus | ESCC | 4.44e-08 | 2.01e-01 | 0.0926 |
| 79639 | TMEM53 | P61T-E | Human | Esophagus | ESCC | 9.60e-05 | 1.48e-01 | 0.099 |
| 79639 | TMEM53 | P62T-E | Human | Esophagus | ESCC | 7.83e-21 | 3.49e-01 | 0.1302 |
| 79639 | TMEM53 | P65T-E | Human | Esophagus | ESCC | 2.07e-08 | 1.71e-01 | 0.0978 |
| 79639 | TMEM53 | P74T-E | Human | Esophagus | ESCC | 6.84e-16 | 4.21e-01 | 0.1479 |
| 79639 | TMEM53 | P75T-E | Human | Esophagus | ESCC | 2.51e-33 | 5.64e-01 | 0.1125 |
| 79639 | TMEM53 | P76T-E | Human | Esophagus | ESCC | 1.30e-15 | 2.73e-01 | 0.1207 |
| 79639 | TMEM53 | P79T-E | Human | Esophagus | ESCC | 9.67e-18 | 2.94e-01 | 0.1154 |
| 79639 | TMEM53 | P80T-E | Human | Esophagus | ESCC | 8.38e-17 | 3.76e-01 | 0.155 |
| 79639 | TMEM53 | P82T-E | Human | Esophagus | ESCC | 1.45e-13 | 6.64e-01 | 0.1072 |
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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 | ||
| 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 |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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| 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 |
| TMEM53 | SNV | Missense_Mutation | novel | c.313G>C | p.Glu105Gln | p.E105Q | Q6P2H8 | protein_coding | tolerated(0.38) | benign(0.342) | TCGA-BH-A1ET-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM53 | SNV | Missense_Mutation | rs769914658 | c.742N>A | p.Val248Met | p.V248M | Q6P2H8 | protein_coding | tolerated(0.12) | probably_damaging(0.931) | TCGA-C8-A12X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM53 | SNV | Missense_Mutation | c.30N>G | p.Ile10Met | p.I10M | Q6P2H8 | protein_coding | deleterious(0) | possibly_damaging(0.65) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| TMEM53 | SNV | Missense_Mutation | rs765679820 | c.712N>T | p.Arg238Cys | p.R238C | Q6P2H8 | protein_coding | deleterious(0.02) | benign(0.007) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| TMEM53 | SNV | Missense_Mutation | novel | c.433N>A | p.Ala145Thr | p.A145T | Q6P2H8 | protein_coding | deleterious(0.03) | benign(0.234) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TMEM53 | SNV | Missense_Mutation | novel | c.479N>T | p.Ala160Val | p.A160V | Q6P2H8 | protein_coding | tolerated(0.71) | benign(0.014) | TCGA-AP-A05O-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| TMEM53 | SNV | Missense_Mutation | rs541061866 | c.661N>A | p.Glu221Lys | p.E221K | Q6P2H8 | protein_coding | tolerated(0.92) | benign(0.007) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| TMEM53 | SNV | Missense_Mutation | novel | c.193N>A | p.Val65Ile | p.V65I | Q6P2H8 | protein_coding | deleterious(0.05) | probably_damaging(0.954) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM53 | SNV | Missense_Mutation | novel | c.491G>A | p.Arg164His | p.R164H | Q6P2H8 | protein_coding | tolerated(0.29) | benign(0.001) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| TMEM53 | SNV | Missense_Mutation | rs572228119 | c.689N>A | p.Arg230His | p.R230H | Q6P2H8 | protein_coding | tolerated(0.69) | benign(0.017) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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