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Gene: TMEM56 |
Gene summary for TMEM56 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM56 | Gene ID | 148534 |
| Gene name | TLC domain containing 4 | |
| Gene Alias | TMEM56 | |
| Cytomap | 1p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | Q96MV1 |
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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 |
| 148534 | TMEM56 | S43 | Human | Liver | Cirrhotic | 9.14e-03 | -1.54e-01 | -0.0187 |
| 148534 | TMEM56 | HCC1_Meng | Human | Liver | HCC | 7.97e-68 | 2.32e-02 | 0.0246 |
| 148534 | TMEM56 | HCC2_Meng | Human | Liver | HCC | 1.04e-07 | -7.82e-02 | 0.0107 |
| 148534 | TMEM56 | HCC1 | Human | Liver | HCC | 8.84e-14 | 2.68e+00 | 0.5336 |
| 148534 | TMEM56 | HCC2 | Human | Liver | HCC | 4.73e-27 | 3.34e+00 | 0.5341 |
| 148534 | TMEM56 | HCC5 | Human | Liver | HCC | 3.82e-13 | 2.12e+00 | 0.4932 |
| 148534 | TMEM56 | Pt14.b | Human | Liver | HCC | 3.43e-02 | 1.82e-01 | 0.018 |
| 148534 | TMEM56 | S014 | Human | Liver | HCC | 1.84e-05 | 4.73e-01 | 0.2254 |
| 148534 | TMEM56 | S015 | Human | Liver | HCC | 7.97e-15 | 8.67e-01 | 0.2375 |
| 148534 | TMEM56 | S016 | Human | Liver | HCC | 5.89e-06 | 5.41e-01 | 0.2243 |
| 148534 | TMEM56 | S028 | Human | Liver | HCC | 1.68e-05 | 4.53e-01 | 0.2503 |
| 148534 | TMEM56 | S029 | Human | Liver | HCC | 1.22e-06 | 5.87e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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 |
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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 |
| TMEM56 | SNV | Missense_Mutation | novel | c.116N>T | p.Asn39Ile | p.N39I | Q96MV1 | protein_coding | tolerated(0.1) | benign(0.031) | TCGA-FI-A2F4-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM56 | insertion | Frame_Shift_Ins | novel | c.400-1_400insA | p.Asn135LysfsTer28 | p.N135Kfs*28 | Q96MV1 | protein_coding | TCGA-AP-A05O-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | ||
| TMEM56 | SNV | Missense_Mutation | c.69N>G | p.Phe23Leu | p.F23L | Q96MV1 | protein_coding | deleterious(0) | possibly_damaging(0.863) | TCGA-DD-AADR-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| TMEM56 | deletion | Frame_Shift_Del | novel | c.9delC | p.Asn4ThrfsTer23 | p.N4Tfs*23 | Q96MV1 | protein_coding | TCGA-DD-AACD-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | ||
| TMEM56 | SNV | Missense_Mutation | novel | c.187N>T | p.Gly63Cys | p.G63C | Q96MV1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-53-7626-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unspecific | Cisplatin | PD |
| TMEM56 | SNV | Missense_Mutation | c.216C>A | p.Phe72Leu | p.F72L | Q96MV1 | protein_coding | deleterious(0.01) | possibly_damaging(0.844) | TCGA-55-7724-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMEM56 | SNV | Missense_Mutation | c.229N>G | p.Lys77Glu | p.K77E | Q96MV1 | protein_coding | tolerated(1) | benign(0.124) | TCGA-78-7220-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| TMEM56 | SNV | Missense_Mutation | rs774641830 | c.433N>T | p.Arg145Cys | p.R145C | Q96MV1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-91-A4BC-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TMEM56 | SNV | Missense_Mutation | novel | c.739C>G | p.His247Asp | p.H247D | Q96MV1 | protein_coding | tolerated(0.18) | benign(0) | TCGA-56-8626-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TMEM56 | SNV | Missense_Mutation | novel | c.210C>G | p.Phe70Leu | p.F70L | Q96MV1 | protein_coding | tolerated(1) | benign(0) | TCGA-98-8021-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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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