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Gene: TM6SF2 |
Gene summary for TM6SF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TM6SF2 | Gene ID | 53345 |
| Gene name | transmembrane 6 superfamily member 2 | |
| Gene Alias | TM6SF2 | |
| Cytomap | 19p13.11 | |
| Gene Type | protein-coding | GO ID | GO:0006629 | UniProtAcc | Q8N8A7 |
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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 |
| 53345 | TM6SF2 | Pat01-B | Human | Stomach | GC | 1.03e-26 | 4.80e-01 | 0.5754 |
| 53345 | TM6SF2 | Pat02-B | Human | Stomach | GC | 9.13e-06 | 1.33e-01 | 0.0368 |
| 53345 | TM6SF2 | Pat03-B | Human | Stomach | GC | 8.94e-22 | 4.53e-01 | 0.3693 |
| 53345 | TM6SF2 | Pat17-B | Human | Stomach | GC | 1.55e-13 | 3.38e-01 | 0.3109 |
| 53345 | TM6SF2 | Pat19-B | Human | Stomach | GC | 3.24e-02 | 1.49e-01 | 0.0826 |
| 53345 | TM6SF2 | SIM_1 | Human | Stomach | SIM | 2.00e-06 | 2.56e-01 | 0.3573 |
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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). |
| 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:0055088 | Stomach | GC | lipid homeostasis | 24/1159 | 167/18723 | 9.86e-05 | 2.00e-03 | 24 |
| GO:0019216 | Stomach | GC | regulation of lipid metabolic process | 37/1159 | 331/18723 | 3.67e-04 | 5.70e-03 | 37 |
| GO:00192161 | Stomach | SIM | regulation of lipid metabolic process | 27/708 | 331/18723 | 1.58e-04 | 3.50e-03 | 27 |
| GO:00550881 | Stomach | SIM | lipid homeostasis | 16/708 | 167/18723 | 6.11e-04 | 9.21e-03 | 16 |
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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 |
| TM6SF2 | SNV | Missense_Mutation | rs370811816 | c.584C>T | p.Ala195Val | p.A195V | Q9BZW4 | protein_coding | tolerated(0.39) | benign(0) | TCGA-A2-A1FV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | SD |
| TM6SF2 | SNV | Missense_Mutation | rs758178350 | c.244G>A | p.Ala82Thr | p.A82T | Q9BZW4 | protein_coding | deleterious(0) | benign(0.181) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| TM6SF2 | SNV | Missense_Mutation | novel | c.822N>G | p.Phe274Leu | p.F274L | Q9BZW4 | protein_coding | tolerated(0.1) | benign(0.285) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TM6SF2 | SNV | Missense_Mutation | c.561G>A | p.Met187Ile | p.M187I | Q9BZW4 | protein_coding | tolerated(0.38) | benign(0.001) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| TM6SF2 | SNV | Missense_Mutation | rs771796358 | c.121N>A | p.Ala41Thr | p.A41T | Q9BZW4 | protein_coding | tolerated(0.23) | benign(0.003) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TM6SF2 | SNV | Missense_Mutation | rs777707469 | c.470N>T | p.Thr157Ile | p.T157I | Q9BZW4 | protein_coding | tolerated(0.33) | benign(0.007) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TM6SF2 | SNV | Missense_Mutation | rs201138158 | c.314N>A | p.Arg105His | p.R105H | Q9BZW4 | protein_coding | tolerated(0.08) | possibly_damaging(0.818) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
| TM6SF2 | SNV | Missense_Mutation | c.1075N>A | p.Ala359Thr | p.A359T | Q9BZW4 | protein_coding | tolerated(0.27) | benign(0.013) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TM6SF2 | SNV | Missense_Mutation | rs771340141 | c.592N>T | p.Arg198Cys | p.R198C | Q9BZW4 | protein_coding | tolerated(0.24) | benign(0) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
| TM6SF2 | SNV | Missense_Mutation | novel | c.832C>T | p.Pro278Ser | p.P278S | Q9BZW4 | protein_coding | deleterious(0) | possibly_damaging(0.903) | TCGA-AJ-A3EL-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 |
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