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Gene: LRRC42 |
Gene summary for LRRC42 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LRRC42 | Gene ID | 115353 |
| Gene name | leucine rich repeat containing 42 | |
| Gene Alias | dJ167A19.4 | |
| Cytomap | 1p32.3 | |
| Gene Type | protein-coding | GO ID | NA | UniProtAcc | Q9Y546 |
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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 |
| 115353 | LRRC42 | LZE4T | Human | Esophagus | ESCC | 2.61e-08 | 2.03e-01 | 0.0811 |
| 115353 | LRRC42 | LZE7T | Human | Esophagus | ESCC | 3.59e-07 | 4.50e-01 | 0.0667 |
| 115353 | LRRC42 | LZE8T | Human | Esophagus | ESCC | 8.60e-10 | 2.72e-01 | 0.067 |
| 115353 | LRRC42 | LZE20T | Human | Esophagus | ESCC | 8.45e-08 | 2.57e-01 | 0.0662 |
| 115353 | LRRC42 | LZE22T | Human | Esophagus | ESCC | 1.17e-06 | 4.25e-01 | 0.068 |
| 115353 | LRRC42 | LZE24T | Human | Esophagus | ESCC | 3.76e-29 | 7.15e-01 | 0.0596 |
| 115353 | LRRC42 | LZE21T | Human | Esophagus | ESCC | 4.48e-04 | 1.40e-01 | 0.0655 |
| 115353 | LRRC42 | LZE6T | Human | Esophagus | ESCC | 3.45e-07 | 3.24e-01 | 0.0845 |
| 115353 | LRRC42 | P1T-E | Human | Esophagus | ESCC | 1.59e-07 | 4.71e-01 | 0.0875 |
| 115353 | LRRC42 | P2T-E | Human | Esophagus | ESCC | 2.12e-22 | 5.08e-01 | 0.1177 |
| 115353 | LRRC42 | P4T-E | Human | Esophagus | ESCC | 7.86e-19 | 4.66e-01 | 0.1323 |
| 115353 | LRRC42 | P5T-E | Human | Esophagus | ESCC | 1.11e-26 | 5.31e-01 | 0.1327 |
| 115353 | LRRC42 | P8T-E | Human | Esophagus | ESCC | 5.20e-34 | 7.05e-01 | 0.0889 |
| 115353 | LRRC42 | P9T-E | Human | Esophagus | ESCC | 3.39e-12 | 2.30e-01 | 0.1131 |
| 115353 | LRRC42 | P10T-E | Human | Esophagus | ESCC | 5.39e-33 | 5.25e-01 | 0.116 |
| 115353 | LRRC42 | P11T-E | Human | Esophagus | ESCC | 2.49e-12 | 4.82e-01 | 0.1426 |
| 115353 | LRRC42 | P12T-E | Human | Esophagus | ESCC | 4.23e-29 | 5.81e-01 | 0.1122 |
| 115353 | LRRC42 | P15T-E | Human | Esophagus | ESCC | 2.55e-32 | 6.04e-01 | 0.1149 |
| 115353 | LRRC42 | P16T-E | Human | Esophagus | ESCC | 2.09e-16 | 2.33e-01 | 0.1153 |
| 115353 | LRRC42 | P17T-E | Human | Esophagus | ESCC | 2.29e-12 | 4.96e-01 | 0.1278 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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 |
| 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 |
| Page: 1 |
| 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 |
| LRRC42 | SNV | Missense_Mutation | c.1155N>G | p.Ser385Arg | p.S385R | Q9Y546 | protein_coding | tolerated(0.65) | benign(0) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | ||
| LRRC42 | SNV | Missense_Mutation | c.78N>T | p.Met26Ile | p.M26I | Q9Y546 | protein_coding | tolerated(0.48) | benign(0.001) | TCGA-A1-A0SP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | ||
| LRRC42 | SNV | Missense_Mutation | c.216N>A | p.Phe72Leu | p.F72L | Q9Y546 | protein_coding | tolerated(0.07) | probably_damaging(0.978) | TCGA-A7-A13E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | bevacizumab | PD | |
| LRRC42 | SNV | Missense_Mutation | c.571C>G | p.Leu191Val | p.L191V | Q9Y546 | protein_coding | deleterious(0.01) | possibly_damaging(0.833) | TCGA-A8-A09M-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | paclitaxel | CR | |
| LRRC42 | SNV | Missense_Mutation | rs759136220 | c.857T>C | p.Leu286Pro | p.L286P | Q9Y546 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-AC-A23C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | chemo | CR |
| LRRC42 | SNV | Missense_Mutation | c.643G>C | p.Asp215His | p.D215H | Q9Y546 | protein_coding | deleterious(0) | possibly_damaging(0.83) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LRRC42 | SNV | Missense_Mutation | novel | c.161N>C | p.Glu54Ala | p.E54A | Q9Y546 | protein_coding | tolerated(0.07) | possibly_damaging(0.775) | TCGA-E9-A54X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LRRC42 | insertion | Nonsense_Mutation | novel | c.706_707insGGCTCAGATTTCTTATGTGAAAACGGAG | p.Thr236ArgfsTer7 | p.T236Rfs*7 | Q9Y546 | protein_coding | TCGA-A8-A07F-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| LRRC42 | SNV | Missense_Mutation | rs749346484 | c.910G>A | p.Glu304Lys | p.E304K | Q9Y546 | protein_coding | deleterious(0.01) | possibly_damaging(0.541) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| LRRC42 | SNV | Missense_Mutation | rs376545473 | c.467G>A | p.Arg156Gln | p.R156Q | Q9Y546 | protein_coding | tolerated(0.08) | possibly_damaging(0.766) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
| Page: 1 2 3 4 |
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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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