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Gene: LIME1 |
Gene summary for LIME1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LIME1 | Gene ID | 54923 |
| Gene name | Lck interacting transmembrane adaptor 1 | |
| Gene Alias | LIME | |
| Cytomap | 20q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0001932 | UniProtAcc | A0A087WT39 |
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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 |
| 54923 | LIME1 | LZE3D | Human | Esophagus | HGIN | 6.21e-05 | 9.26e-01 | 0.0668 |
| 54923 | LIME1 | LZE4T | Human | Esophagus | ESCC | 5.68e-07 | 2.32e-01 | 0.0811 |
| 54923 | LIME1 | LZE7T | Human | Esophagus | ESCC | 6.28e-20 | 7.98e-01 | 0.0667 |
| 54923 | LIME1 | LZE8T | Human | Esophagus | ESCC | 1.35e-07 | 2.76e-01 | 0.067 |
| 54923 | LIME1 | LZE22D1 | Human | Esophagus | HGIN | 2.88e-06 | 4.10e-01 | 0.0595 |
| 54923 | LIME1 | LZE22T | Human | Esophagus | ESCC | 1.57e-03 | 3.08e-01 | 0.068 |
| 54923 | LIME1 | LZE24T | Human | Esophagus | ESCC | 2.14e-21 | 5.56e-01 | 0.0596 |
| 54923 | LIME1 | LZE22D3 | Human | Esophagus | HGIN | 3.01e-07 | 5.85e-01 | 0.0653 |
| 54923 | LIME1 | LZE6T | Human | Esophagus | ESCC | 1.71e-05 | 3.26e-01 | 0.0845 |
| 54923 | LIME1 | P1T-E | Human | Esophagus | ESCC | 7.11e-04 | 2.04e-01 | 0.0875 |
| 54923 | LIME1 | P2T-E | Human | Esophagus | ESCC | 4.40e-09 | 1.70e-01 | 0.1177 |
| 54923 | LIME1 | P4T-E | Human | Esophagus | ESCC | 1.36e-04 | 1.70e-01 | 0.1323 |
| 54923 | LIME1 | P8T-E | Human | Esophagus | ESCC | 3.97e-04 | 1.04e-01 | 0.0889 |
| 54923 | LIME1 | P10T-E | Human | Esophagus | ESCC | 8.08e-19 | 3.27e-01 | 0.116 |
| 54923 | LIME1 | P12T-E | Human | Esophagus | ESCC | 3.97e-04 | 1.19e-01 | 0.1122 |
| 54923 | LIME1 | P17T-E | Human | Esophagus | ESCC | 4.79e-04 | 2.38e-01 | 0.1278 |
| 54923 | LIME1 | P20T-E | Human | Esophagus | ESCC | 1.19e-07 | 2.02e-01 | 0.1124 |
| 54923 | LIME1 | P21T-E | Human | Esophagus | ESCC | 1.53e-19 | 3.67e-01 | 0.1617 |
| 54923 | LIME1 | P31T-E | Human | Esophagus | ESCC | 4.16e-22 | 3.31e-01 | 0.1251 |
| 54923 | LIME1 | P40T-E | Human | Esophagus | ESCC | 2.37e-02 | 1.31e-01 | 0.109 |
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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 | ||
| 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 | ||
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00508512 | Stomach | CSG | antigen receptor-mediated signaling pathway | 24/1034 | 240/18723 | 3.65e-03 | 3.26e-02 | 24 |
| GO:00022531 | Stomach | CSG | activation of immune response | 33/1034 | 375/18723 | 5.70e-03 | 4.54e-02 | 33 |
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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 |
| LIME1 | SNV | Missense_Mutation | c.580N>A | p.Ala194Thr | p.A194T | Q9H400 | protein_coding | tolerated(0.67) | benign(0.006) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LIME1 | SNV | Missense_Mutation | novel | c.445N>T | p.Gly149Trp | p.G149W | Q9H400 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AJ-A3OJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| LIME1 | SNV | Missense_Mutation | novel | c.646G>T | p.Asp216Tyr | p.D216Y | Q9H400 | protein_coding | deleterious(0.01) | possibly_damaging(0.808) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIME1 | SNV | Missense_Mutation | rs776251119 | c.716C>T | p.Pro239Leu | p.P239L | Q9H400 | protein_coding | deleterious(0.03) | benign(0.014) | TCGA-D1-A1NZ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIME1 | SNV | Missense_Mutation | novel | c.517C>T | p.Arg173Cys | p.R173C | Q9H400 | protein_coding | tolerated(0.12) | possibly_damaging(0.735) | TCGA-FI-A2D0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIME1 | deletion | Frame_Shift_Del | novel | c.487delG | p.Val163TrpfsTer28 | p.V163Wfs*28 | Q9H400 | protein_coding | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD | ||
| LIME1 | SNV | Missense_Mutation | c.127N>T | p.Arg43Trp | p.R43W | Q9H400 | protein_coding | deleterious(0.01) | benign(0.038) | TCGA-86-8358-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| LIME1 | SNV | Missense_Mutation | novel | c.86C>T | p.Thr29Ile | p.T29I | Q9H400 | protein_coding | deleterious(0) | possibly_damaging(0.744) | TCGA-NC-A5HG-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Chemotherapy | cisplatin | CR |
| LIME1 | SNV | Missense_Mutation | rs774768440 | c.592N>A | p.Val198Ile | p.V198I | Q9H400 | protein_coding | tolerated(1) | benign(0.003) | TCGA-BA-A6DI-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
| LIME1 | SNV | Missense_Mutation | c.656N>G | p.Asp219Gly | p.D219G | Q9H400 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-EJ-A65M-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 6 | 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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