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Gene: LIN54 |
Gene summary for LIN54 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LIN54 | Gene ID | 132660 |
| Gene name | lin-54 DREAM MuvB core complex component | |
| Gene Alias | CXCDC1 | |
| Cytomap | 4q21.22 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q6MZP7 |
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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 |
| 132660 | LIN54 | LZE2T | Human | Esophagus | ESCC | 7.49e-04 | 3.40e-01 | 0.082 |
| 132660 | LIN54 | LZE4T | Human | Esophagus | ESCC | 6.45e-05 | 1.08e-01 | 0.0811 |
| 132660 | LIN54 | LZE24T | Human | Esophagus | ESCC | 1.57e-06 | 1.12e-01 | 0.0596 |
| 132660 | LIN54 | P2T-E | Human | Esophagus | ESCC | 1.04e-17 | 3.19e-01 | 0.1177 |
| 132660 | LIN54 | P4T-E | Human | Esophagus | ESCC | 4.92e-03 | 1.13e-01 | 0.1323 |
| 132660 | LIN54 | P5T-E | Human | Esophagus | ESCC | 7.34e-03 | 8.39e-02 | 0.1327 |
| 132660 | LIN54 | P8T-E | Human | Esophagus | ESCC | 2.10e-03 | 1.17e-01 | 0.0889 |
| 132660 | LIN54 | P9T-E | Human | Esophagus | ESCC | 4.95e-04 | 9.88e-02 | 0.1131 |
| 132660 | LIN54 | P10T-E | Human | Esophagus | ESCC | 2.36e-03 | 7.48e-02 | 0.116 |
| 132660 | LIN54 | P11T-E | Human | Esophagus | ESCC | 4.81e-02 | 1.70e-01 | 0.1426 |
| 132660 | LIN54 | P12T-E | Human | Esophagus | ESCC | 6.79e-08 | 1.61e-01 | 0.1122 |
| 132660 | LIN54 | P15T-E | Human | Esophagus | ESCC | 7.40e-12 | 1.97e-01 | 0.1149 |
| 132660 | LIN54 | P16T-E | Human | Esophagus | ESCC | 3.86e-11 | 1.70e-01 | 0.1153 |
| 132660 | LIN54 | P17T-E | Human | Esophagus | ESCC | 5.49e-03 | 1.18e-01 | 0.1278 |
| 132660 | LIN54 | P21T-E | Human | Esophagus | ESCC | 2.84e-05 | 7.78e-02 | 0.1617 |
| 132660 | LIN54 | P22T-E | Human | Esophagus | ESCC | 6.16e-04 | 4.45e-02 | 0.1236 |
| 132660 | LIN54 | P23T-E | Human | Esophagus | ESCC | 4.81e-10 | 2.19e-01 | 0.108 |
| 132660 | LIN54 | P24T-E | Human | Esophagus | ESCC | 7.94e-05 | 9.30e-02 | 0.1287 |
| 132660 | LIN54 | P26T-E | Human | Esophagus | ESCC | 8.89e-10 | 1.84e-01 | 0.1276 |
| 132660 | LIN54 | P27T-E | Human | Esophagus | ESCC | 6.44e-04 | 1.18e-01 | 0.1055 |
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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 |
| ∗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:000632517 | Esophagus | ESCC | chromatin organization | 240/8552 | 409/18723 | 6.52e-08 | 1.14e-06 | 240 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0421829 | Esophagus | ESCC | Cellular senescence | 119/4205 | 156/8465 | 5.89e-12 | 9.40e-11 | 4.81e-11 | 119 |
| hsa0421838 | Esophagus | ESCC | Cellular senescence | 119/4205 | 156/8465 | 5.89e-12 | 9.40e-11 | 4.81e-11 | 119 |
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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 |
| LIN54 | SNV | Missense_Mutation | c.1744N>G | p.Lys582Glu | p.K582E | Q6MZP7 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-D1-A160-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LIN54 | SNV | Missense_Mutation | c.1808G>A | p.Arg603Gln | p.R603Q | Q6MZP7 | protein_coding | deleterious(0) | probably_damaging(0.949) | TCGA-D1-A2G0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LIN54 | SNV | Missense_Mutation | novel | c.1415N>C | p.Val472Ala | p.V472A | Q6MZP7 | protein_coding | deleterious(0) | benign(0.428) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| LIN54 | SNV | Missense_Mutation | novel | c.227N>C | p.Val76Ala | p.V76A | Q6MZP7 | protein_coding | tolerated_low_confidence(0.11) | benign(0) | TCGA-EO-A3AY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| LIN54 | SNV | Missense_Mutation | novel | c.1930N>G | p.Leu644Val | p.L644V | Q6MZP7 | protein_coding | deleterious(0.04) | benign(0.189) | TCGA-EY-A1GD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIN54 | SNV | Missense_Mutation | novel | c.2173G>A | p.Glu725Lys | p.E725K | Q6MZP7 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIN54 | SNV | Missense_Mutation | novel | c.1138N>T | p.Pro380Ser | p.P380S | Q6MZP7 | protein_coding | tolerated(0.17) | benign(0.058) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| LIN54 | SNV | Missense_Mutation | novel | c.371N>T | p.Ser124Phe | p.S124F | Q6MZP7 | protein_coding | deleterious_low_confidence(0) | benign(0.094) | TCGA-FI-A2F4-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIN54 | insertion | Frame_Shift_Ins | novel | c.1036_1037insACACTGTGTA | p.Pro346HisfsTer29 | p.P346Hfs*29 | Q6MZP7 | protein_coding | TCGA-A5-A0R8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| LIN54 | insertion | Frame_Shift_Ins | novel | c.1029_1030insC | p.Thr344HisfsTer28 | p.T344Hfs*28 | Q6MZP7 | protein_coding | TCGA-A5-A0R9-01 | 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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