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Gene: LCE3D |
Gene summary for LCE3D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LCE3D | Gene ID | 84648 |
| Gene name | late cornified envelope 3D | |
| Gene Alias | LEP16 | |
| Cytomap | 1q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0007275 | UniProtAcc | Q9BYE3 |
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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 |
| 84648 | LCE3D | C43 | Human | Oral cavity | OSCC | 6.42e-03 | 1.03e+00 | 0.1704 |
| 84648 | LCE3D | SYSMH3 | Human | Oral cavity | OSCC | 1.48e-35 | 5.76e-01 | 0.2442 |
| 84648 | LCE3D | SYSMH5 | Human | Oral cavity | OSCC | 2.77e-23 | 6.71e-01 | 0.0647 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| Stomach | WIM |  |
| Stomach | SIM |  |
| Liver | NAFLD |  |
| Liver | Cirrhotic |  |
| Liver | HCC |  |
| ∗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:00435887 | Oral cavity | OSCC | skin development | 143/7305 | 263/18723 | 2.77e-07 | 4.27e-06 | 143 |
| GO:00085449 | Oral cavity | OSCC | epidermis development | 171/7305 | 324/18723 | 2.89e-07 | 4.43e-06 | 171 |
| GO:00302166 | Oral cavity | OSCC | keratinocyte differentiation | 81/7305 | 139/18723 | 3.16e-06 | 3.81e-05 | 81 |
| GO:00099139 | Oral cavity | OSCC | epidermal cell differentiation | 109/7305 | 202/18723 | 1.08e-05 | 1.14e-04 | 109 |
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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 |
| LCE3D | SNV | Missense_Mutation | rs147417899 | c.193C>T | p.Arg65Cys | p.R65C | Q9BYE3 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.649) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LCE3D | SNV | Missense_Mutation | rs754669874 | c.185N>A | p.Arg62Gln | p.R62Q | Q9BYE3 | protein_coding | tolerated_low_confidence(0.22) | benign(0.024) | TCGA-V7-A7HQ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | letrozole | CR |
| LCE3D | SNV | Missense_Mutation | novel | c.101C>A | p.Ser34Tyr | p.S34Y | Q9BYE3 | protein_coding | deleterious_low_confidence(0.03) | possibly_damaging(0.648) | TCGA-VS-A9UV-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | PD |
| LCE3D | SNV | Missense_Mutation | novel | c.62N>T | p.Cys21Phe | p.C21F | Q9BYE3 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LCE3D | SNV | Missense_Mutation | c.152N>T | p.Gly51Val | p.G51V | Q9BYE3 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.666) | TCGA-QG-A5Z2-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| LCE3D | SNV | Missense_Mutation | rs145962377 | c.151G>A | p.Gly51Ser | p.G51S | Q9BYE3 | protein_coding | tolerated_low_confidence(0.08) | benign(0.036) | TCGA-AF-3913-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | xeloda | PD |
| LCE3D | SNV | Missense_Mutation | rs371301948 | c.191G>A | p.Arg64Gln | p.R64Q | Q9BYE3 | protein_coding | tolerated_low_confidence(0.12) | benign(0.005) | TCGA-DC-6683-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD |
| LCE3D | SNV | Missense_Mutation | rs749727744 | c.176N>A | p.Arg59His | p.R59H | Q9BYE3 | protein_coding | tolerated_low_confidence(0.18) | benign(0) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LCE3D | SNV | Missense_Mutation | c.221N>A | p.Gly74Asp | p.G74D | Q9BYE3 | protein_coding | deleterious_low_confidence(0.03) | benign(0.094) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| LCE3D | SNV | Missense_Mutation | novel | c.85N>G | p.Cys29Gly | p.C29G | Q9BYE3 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.605) | TCGA-BS-A0UF-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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