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Gene: LRCH4 |
Gene summary for LRCH4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LRCH4 | Gene ID | 4034 |
| Gene name | leucine rich repeats and calponin homology domain containing 4 | |
| Gene Alias | LRN | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0007275 | UniProtAcc | O75427 |
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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 |
| 4034 | LRCH4 | LZE7T | Human | Esophagus | ESCC | 2.56e-05 | 2.13e-01 | 0.0667 |
| 4034 | LRCH4 | LZE22T | Human | Esophagus | ESCC | 1.54e-04 | 3.63e-01 | 0.068 |
| 4034 | LRCH4 | LZE24T | Human | Esophagus | ESCC | 3.74e-07 | 1.85e-01 | 0.0596 |
| 4034 | LRCH4 | P1T-E | Human | Esophagus | ESCC | 2.97e-02 | 1.65e-01 | 0.0875 |
| 4034 | LRCH4 | P2T-E | Human | Esophagus | ESCC | 1.77e-22 | 3.39e-01 | 0.1177 |
| 4034 | LRCH4 | P4T-E | Human | Esophagus | ESCC | 2.20e-02 | 9.45e-02 | 0.1323 |
| 4034 | LRCH4 | P8T-E | Human | Esophagus | ESCC | 9.53e-09 | 2.17e-01 | 0.0889 |
| 4034 | LRCH4 | P10T-E | Human | Esophagus | ESCC | 4.30e-10 | 2.24e-01 | 0.116 |
| 4034 | LRCH4 | P11T-E | Human | Esophagus | ESCC | 2.06e-07 | 3.08e-01 | 0.1426 |
| 4034 | LRCH4 | P12T-E | Human | Esophagus | ESCC | 5.00e-17 | 2.87e-01 | 0.1122 |
| 4034 | LRCH4 | P15T-E | Human | Esophagus | ESCC | 2.31e-15 | 3.46e-01 | 0.1149 |
| 4034 | LRCH4 | P16T-E | Human | Esophagus | ESCC | 8.56e-12 | 2.64e-01 | 0.1153 |
| 4034 | LRCH4 | P17T-E | Human | Esophagus | ESCC | 1.45e-12 | 3.73e-01 | 0.1278 |
| 4034 | LRCH4 | P20T-E | Human | Esophagus | ESCC | 3.20e-07 | 2.02e-01 | 0.1124 |
| 4034 | LRCH4 | P21T-E | Human | Esophagus | ESCC | 1.76e-12 | 2.31e-01 | 0.1617 |
| 4034 | LRCH4 | P22T-E | Human | Esophagus | ESCC | 7.90e-03 | 8.50e-02 | 0.1236 |
| 4034 | LRCH4 | P23T-E | Human | Esophagus | ESCC | 5.34e-19 | 4.13e-01 | 0.108 |
| 4034 | LRCH4 | P24T-E | Human | Esophagus | ESCC | 1.66e-02 | 8.88e-02 | 0.1287 |
| 4034 | LRCH4 | P26T-E | Human | Esophagus | ESCC | 8.40e-04 | 1.16e-01 | 0.1276 |
| 4034 | LRCH4 | P27T-E | Human | Esophagus | ESCC | 3.60e-13 | 2.24e-01 | 0.1055 |
| Page: 1 2 3 4 5 |
| 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 | ||
| 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 |
| LRCH4 | SNV | Missense_Mutation | c.1018N>A | p.Glu340Lys | p.E340K | O75427 | protein_coding | deleterious(0.01) | possibly_damaging(0.493) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LRCH4 | SNV | Missense_Mutation | novel | c.2005C>A | p.Leu669Ile | p.L669I | O75427 | protein_coding | tolerated(0.24) | benign(0.01) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LRCH4 | SNV | Missense_Mutation | c.851N>G | p.Pro284Arg | p.P284R | O75427 | protein_coding | tolerated(0.12) | possibly_damaging(0.648) | TCGA-VS-A9V5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
| LRCH4 | SNV | Missense_Mutation | c.122C>T | p.Ala41Val | p.A41V | O75427 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LRCH4 | SNV | Missense_Mutation | rs375173199 | c.1406N>T | p.Ala469Val | p.A469V | O75427 | protein_coding | tolerated(0.39) | benign(0.049) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| LRCH4 | SNV | Missense_Mutation | rs191101243 | c.998N>A | p.Arg333Gln | p.R333Q | O75427 | protein_coding | tolerated(0.18) | benign(0.035) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LRCH4 | SNV | Missense_Mutation | c.1253A>G | p.Gln418Arg | p.Q418R | O75427 | protein_coding | tolerated(0.06) | benign(0.003) | TCGA-CM-5861-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| LRCH4 | SNV | Missense_Mutation | rs750048626 | c.1072G>A | p.Asp358Asn | p.D358N | O75427 | protein_coding | deleterious(0.03) | possibly_damaging(0.906) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LRCH4 | SNV | Missense_Mutation | rs765137965 | c.845C>T | p.Pro282Leu | p.P282L | O75427 | protein_coding | deleterious(0.02) | benign(0.334) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LRCH4 | SNV | Missense_Mutation | novel | c.282G>T | p.Glu94Asp | p.E94D | O75427 | protein_coding | deleterious(0.01) | probably_damaging(0.957) | TCGA-A5-A1OF-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 |
| Page: 1 |
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