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Gene: TNFRSF6B |
Gene summary for TNFRSF6B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TNFRSF6B | Gene ID | 8771 |
| Gene name | TNF receptor superfamily member 6b | |
| Gene Alias | DCR3 | |
| Cytomap | 20q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0006915 | UniProtAcc | O95407 |
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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 |
| 8771 | TNFRSF6B | Pat02-B | Human | Stomach | GC | 5.43e-16 | 3.05e-01 | 0.0368 |
| 8771 | TNFRSF6B | Pat06-B | Human | Stomach | GC | 1.32e-12 | 3.17e-01 | -0.1961 |
| 8771 | TNFRSF6B | Pat08-B | Human | Stomach | GC | 1.40e-04 | 3.25e-01 | 0.0182 |
| 8771 | TNFRSF6B | Pat10-B | Human | Stomach | GC | 1.73e-04 | 3.79e-01 | 0.084 |
| 8771 | TNFRSF6B | Pat11-B | Human | Stomach | GC | 2.41e-04 | 2.55e-01 | -0.182 |
| 8771 | TNFRSF6B | Pat12-B | Human | Stomach | GC | 8.22e-37 | 7.20e-01 | 0.0325 |
| 8771 | TNFRSF6B | Pat15-B | Human | Stomach | GC | 1.34e-08 | 3.28e-01 | -0.0778 |
| 8771 | TNFRSF6B | Pat16-B | Human | Stomach | GC | 3.97e-04 | 1.98e-01 | 0.1918 |
| 8771 | TNFRSF6B | Pat18-B | Human | Stomach | GC | 7.15e-04 | 1.68e-01 | -0.0432 |
| 8771 | TNFRSF6B | Pat19-B | Human | Stomach | GC | 3.54e-06 | 2.76e-01 | 0.0826 |
| 8771 | TNFRSF6B | Pat24-B | Human | Stomach | GC | 1.12e-03 | 1.97e-01 | -0.1184 |
| 8771 | TNFRSF6B | Pat26-A | Human | Stomach | CSG | 4.15e-05 | 1.69e-01 | -0.2402 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia |
| ∗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 |
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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 |
| TNFRSF6B | SNV | Missense_Mutation | rs572993898 | c.137N>A | p.Arg46Gln | p.R46Q | O95407 | protein_coding | tolerated(0.34) | benign(0.007) | TCGA-D8-A1XV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TNFRSF6B | SNV | Missense_Mutation | novel | c.614N>C | p.Val205Ala | p.V205A | O95407 | protein_coding | tolerated(0.79) | benign(0) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TNFRSF6B | deletion | In_Frame_Del | c.471_473delNNN | p.Phe158del | p.F158del | O95407 | protein_coding | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |||
| TNFRSF6B | deletion | Frame_Shift_Del | c.459delN | p.Pro155GlnfsTer101 | p.P155Qfs*101 | O95407 | protein_coding | TCGA-D5-6927-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |||
| TNFRSF6B | SNV | Missense_Mutation | rs774448942 | c.136C>T | p.Arg46Trp | p.R46W | O95407 | protein_coding | deleterious(0.04) | benign(0) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TNFRSF6B | insertion | Frame_Shift_Ins | rs770578181 | c.458_459insC | p.Gly156ArgfsTer35 | p.G156Rfs*35 | O95407 | protein_coding | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TNFRSF6B | SNV | Missense_Mutation | c.746N>A | p.Gly249Asp | p.G249D | O95407 | protein_coding | tolerated(0.7) | possibly_damaging(0.559) | TCGA-G3-A25Y-01 | Liver | liver hepatocellular carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| TNFRSF6B | SNV | Missense_Mutation | novel | c.269N>G | p.Tyr90Cys | p.Y90C | O95407 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-WQ-A9G7-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| TNFRSF6B | SNV | Missense_Mutation | novel | c.827N>C | p.Leu276Pro | p.L276P | O95407 | protein_coding | deleterious(0) | possibly_damaging(0.884) | TCGA-L3-A524-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TNFRSF6B | SNV | Missense_Mutation | rs764972813 | c.678N>G | p.Ile226Met | p.I226M | O95407 | protein_coding | tolerated(0.18) | benign(0.031) | TCGA-BA-4074-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | 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 |
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