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Gene: LONRF3 |
Gene summary for LONRF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LONRF3 | Gene ID | 79836 |
| Gene name | LON peptidase N-terminal domain and ring finger 3 | |
| Gene Alias | RNF127 | |
| Cytomap | Xq24 | |
| Gene Type | protein-coding | GO ID | GO:0003674 | UniProtAcc | A8K2D3 |
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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 |
| 79836 | LONRF3 | male-WTA | Human | Thyroid | PTC | 1.87e-02 | -1.33e-01 | 0.1037 |
| 79836 | LONRF3 | PTC04 | Human | Thyroid | PTC | 6.40e-13 | 3.01e-01 | 0.1927 |
| 79836 | LONRF3 | PTC07 | Human | Thyroid | PTC | 5.48e-10 | 1.74e-01 | 0.2044 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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 |
| Oral cavity | OSCC |  |
| Oral cavity | LP |  |
| Oral cavity | EOLP |  |
| Oral cavity | NEOLP |  |
| Esophagus | HGIN |  |
| ∗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 |
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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 |
| LONRF3 | SNV | Missense_Mutation | c.1214C>A | p.Ser405Tyr | p.S405Y | Q496Y0 | protein_coding | deleterious(0.01) | possibly_damaging(0.492) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| LONRF3 | SNV | Missense_Mutation | c.1192N>C | p.Glu398Gln | p.E398Q | Q496Y0 | protein_coding | tolerated(0.09) | benign(0.103) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| LONRF3 | SNV | Missense_Mutation | c.176C>T | p.Ser59Phe | p.S59F | Q496Y0 | protein_coding | deleterious(0.03) | benign(0.015) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| LONRF3 | SNV | Missense_Mutation | c.1186N>C | p.Glu396Gln | p.E396Q | Q496Y0 | protein_coding | tolerated(0.31) | benign(0.003) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| LONRF3 | SNV | Missense_Mutation | c.1465N>G | p.Lys489Glu | p.K489E | Q496Y0 | protein_coding | deleterious(0) | possibly_damaging(0.579) | TCGA-D8-A1JI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD | |
| LONRF3 | SNV | Missense_Mutation | c.1751N>A | p.Arg584His | p.R584H | Q496Y0 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E2-A15E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| LONRF3 | insertion | In_Frame_Ins | novel | c.1622_1623insCAGATTACTCCAATATGTGGGTCATTTGACTTG | p.Leu541_Tyr542insArgLeuLeuGlnTyrValGlyHisLeuThrCys | p.L541_Y542insRLLQYVGHLTC | Q496Y0 | protein_coding | TCGA-AO-A0JM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| LONRF3 | SNV | Missense_Mutation | novel | c.1616N>T | p.Arg539Met | p.R539M | Q496Y0 | protein_coding | deleterious(0) | possibly_damaging(0.682) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LONRF3 | SNV | Missense_Mutation | novel | c.1900N>T | p.Arg634Cys | p.R634C | Q496Y0 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LONRF3 | SNV | Missense_Mutation | c.2158N>T | p.Met720Leu | p.M720L | Q496Y0 | protein_coding | tolerated(1) | benign(0) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | 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 |
| Page: 1 |
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