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Gene: TREM2 |
Gene summary for TREM2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TREM2 | Gene ID | 54209 |
| Gene name | triggering receptor expressed on myeloid cells 2 | |
| Gene Alias | PLOSL2 | |
| Cytomap | 6p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q9NZC2 |
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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 |
| 54209 | TREM2 | LZE6T | Human | Esophagus | ESCC | 9.93e-10 | 8.88e-01 | 0.0845 |
| 54209 | TREM2 | P16T-E | Human | Esophagus | ESCC | 6.19e-93 | 3.57e+00 | 0.1153 |
| 54209 | TREM2 | P17T-E | Human | Esophagus | ESCC | 4.70e-13 | 1.06e+00 | 0.1278 |
| 54209 | TREM2 | P22T-E | Human | Esophagus | ESCC | 7.95e-19 | 4.67e-01 | 0.1236 |
| 54209 | TREM2 | P56T-E | Human | Esophagus | ESCC | 8.17e-06 | 1.05e+00 | 0.1613 |
| 54209 | TREM2 | P65T-E | Human | Esophagus | ESCC | 3.48e-10 | 6.06e-01 | 0.0978 |
| 54209 | TREM2 | P74T-E | Human | Esophagus | ESCC | 1.66e-21 | 1.07e+00 | 0.1479 |
| 54209 | TREM2 | P76T-E | Human | Esophagus | ESCC | 1.99e-15 | 1.48e+00 | 0.1207 |
| 54209 | TREM2 | P83T-E | Human | Esophagus | ESCC | 3.65e-03 | 2.26e-01 | 0.1738 |
| 54209 | TREM2 | P107T-E | Human | Esophagus | ESCC | 4.07e-24 | 1.21e+00 | 0.171 |
| 54209 | TREM2 | C04 | Human | Oral cavity | OSCC | 1.62e-38 | 2.16e+00 | 0.2633 |
| 54209 | TREM2 | C21 | Human | Oral cavity | OSCC | 4.07e-23 | 7.57e-01 | 0.2678 |
| 54209 | TREM2 | C30 | Human | Oral cavity | OSCC | 8.42e-14 | 6.37e-01 | 0.3055 |
| 54209 | TREM2 | C06 | Human | Oral cavity | OSCC | 6.22e-04 | 7.50e-01 | 0.2699 |
| 54209 | TREM2 | C07 | Human | Oral cavity | OSCC | 8.27e-07 | 2.11e+00 | 0.2491 |
| 54209 | TREM2 | LN22 | Human | Oral cavity | OSCC | 3.59e-16 | 2.07e+00 | 0.1733 |
| 54209 | TREM2 | SYSMH2 | Human | Oral cavity | OSCC | 9.26e-07 | 2.78e-01 | 0.2326 |
| 54209 | TREM2 | SYSMH3 | Human | Oral cavity | OSCC | 1.63e-40 | 1.28e+00 | 0.2442 |
| 54209 | TREM2 | SYSMH6 | Human | Oral cavity | OSCC | 1.66e-02 | 4.92e-01 | 0.1275 |
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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 | ||
| 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). |
| 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:007132616 | Oral cavity | OSCC | cellular response to monosaccharide stimulus | 79/7305 | 154/18723 | 1.27e-03 | 6.33e-03 | 79 |
| GO:004639017 | Oral cavity | OSCC | ribose phosphate biosynthetic process | 95/7305 | 190/18723 | 1.30e-03 | 6.46e-03 | 95 |
| GO:003647319 | Oral cavity | OSCC | cell death in response to oxidative stress | 52/7305 | 95/18723 | 1.33e-03 | 6.62e-03 | 52 |
| GO:00716929 | Oral cavity | OSCC | protein localization to extracellular region | 172/7305 | 368/18723 | 1.40e-03 | 6.79e-03 | 172 |
| GO:003350016 | Oral cavity | OSCC | carbohydrate homeostasis | 125/7305 | 259/18723 | 1.44e-03 | 6.97e-03 | 125 |
| GO:00100015 | Oral cavity | OSCC | glial cell differentiation | 110/7305 | 225/18723 | 1.56e-03 | 7.45e-03 | 110 |
| GO:00199154 | Oral cavity | OSCC | lipid storage | 48/7305 | 87/18723 | 1.60e-03 | 7.62e-03 | 48 |
| GO:00486784 | Oral cavity | OSCC | response to axon injury | 46/7305 | 83/18723 | 1.76e-03 | 8.31e-03 | 46 |
| GO:000181910 | Oral cavity | OSCC | positive regulation of cytokine production | 213/7305 | 467/18723 | 1.93e-03 | 8.96e-03 | 213 |
| GO:00622076 | Oral cavity | OSCC | regulation of pattern recognition receptor signaling pathway | 56/7305 | 105/18723 | 1.99e-03 | 9.23e-03 | 56 |
| GO:004563910 | Oral cavity | OSCC | positive regulation of myeloid cell differentiation | 55/7305 | 103/18723 | 2.10e-03 | 9.64e-03 | 55 |
| GO:007132217 | Oral cavity | OSCC | cellular response to carbohydrate stimulus | 82/7305 | 163/18723 | 2.14e-03 | 9.81e-03 | 82 |
| GO:000250410 | Oral cavity | OSCC | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 23/7305 | 36/18723 | 2.19e-03 | 9.95e-03 | 23 |
| GO:00972424 | Oral cavity | OSCC | amyloid-beta clearance | 24/7305 | 38/18723 | 2.21e-03 | 1.00e-02 | 24 |
| GO:19012224 | Oral cavity | OSCC | regulation of NIK/NF-kappaB signaling | 59/7305 | 112/18723 | 2.25e-03 | 1.00e-02 | 59 |
| GO:00022243 | Oral cavity | OSCC | toll-like receptor signaling pathway | 63/7305 | 121/18723 | 2.36e-03 | 1.04e-02 | 63 |
| GO:005071414 | Oral cavity | OSCC | positive regulation of protein secretion | 70/7305 | 137/18723 | 2.64e-03 | 1.16e-02 | 70 |
| GO:00027646 | Oral cavity | OSCC | immune response-regulating signaling pathway | 212/7305 | 468/18723 | 2.93e-03 | 1.27e-02 | 212 |
| GO:00192167 | Oral cavity | OSCC | regulation of lipid metabolic process | 154/7305 | 331/18723 | 3.00e-03 | 1.30e-02 | 154 |
| GO:00620128 | Oral cavity | OSCC | regulation of small molecule metabolic process | 155/7305 | 334/18723 | 3.30e-03 | 1.41e-02 | 155 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa043806 | Oral cavity | OSCC | Osteoclast differentiation | 73/3704 | 128/8465 | 1.60e-03 | 4.44e-03 | 2.26e-03 | 73 |
| hsa0438011 | Oral cavity | OSCC | Osteoclast differentiation | 73/3704 | 128/8465 | 1.60e-03 | 4.44e-03 | 2.26e-03 | 73 |
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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. |
| 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 |
| TREM2 | SNV | Missense_Mutation | novel | c.586N>T | p.Ala196Ser | p.A196S | Q9NZC2 | protein_coding | tolerated(0.05) | benign(0.081) | TCGA-VS-A952-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| TREM2 | SNV | Missense_Mutation | c.523N>G | p.Ile175Val | p.I175V | Q9NZC2 | protein_coding | tolerated(0.59) | benign(0.015) | TCGA-D5-6929-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatinum+ | SD | |
| TREM2 | SNV | Missense_Mutation | c.101N>C | p.Val34Ala | p.V34A | Q9NZC2 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-G4-6586-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TREM2 | SNV | Missense_Mutation | c.636N>A | p.Asp212Glu | p.D212E | Q9NZC2 | protein_coding | tolerated(0.1) | benign(0.012) | TCGA-AG-A023-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| TREM2 | SNV | Missense_Mutation | c.538N>T | p.Ala180Ser | p.A180S | Q9NZC2 | protein_coding | deleterious(0.03) | possibly_damaging(0.669) | TCGA-AJ-A3BG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | |
| TREM2 | SNV | Missense_Mutation | rs764373520 | c.247G>A | p.Ala83Thr | p.A83T | Q9NZC2 | protein_coding | deleterious(0.04) | benign(0.158) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TREM2 | SNV | Missense_Mutation | c.550N>T | p.Leu184Phe | p.L184F | Q9NZC2 | protein_coding | tolerated(0.08) | benign(0.046) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| TREM2 | SNV | Missense_Mutation | novel | c.262A>C | p.Thr88Pro | p.T88P | Q9NZC2 | protein_coding | tolerated(0.11) | possibly_damaging(0.522) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TREM2 | SNV | Missense_Mutation | c.319C>T | p.Leu107Phe | p.L107F | Q9NZC2 | protein_coding | tolerated(0.06) | benign(0.159) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| TREM2 | SNV | Missense_Mutation | c.335G>A | p.Ser112Asn | p.S112N | Q9NZC2 | protein_coding | deleterious(0.01) | possibly_damaging(0.455) | TCGA-B5-A11E-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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