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Gene: LRTOMT |
Gene summary for LRTOMT |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRTOMT | Gene ID | 220074 |
Gene name | leucine rich transmembrane and O-methyltransferase domain containing | |
Gene Alias | CFAP111 | |
Cytomap | 11q13.4 | |
Gene Type | protein-coding | GO ID | GO:0001505 | UniProtAcc | Q8WZ04 |
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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 |
220074 | LRTOMT | LZE24T | Human | Esophagus | ESCC | 2.49e-04 | 2.08e-01 | 0.0596 |
220074 | LRTOMT | P2T-E | Human | Esophagus | ESCC | 4.25e-15 | 3.21e-01 | 0.1177 |
220074 | LRTOMT | P4T-E | Human | Esophagus | ESCC | 1.73e-09 | 1.99e-01 | 0.1323 |
220074 | LRTOMT | P9T-E | Human | Esophagus | ESCC | 1.04e-06 | 1.04e-01 | 0.1131 |
220074 | LRTOMT | P10T-E | Human | Esophagus | ESCC | 1.76e-09 | 9.71e-02 | 0.116 |
220074 | LRTOMT | P12T-E | Human | Esophagus | ESCC | 2.03e-09 | 8.87e-02 | 0.1122 |
220074 | LRTOMT | P15T-E | Human | Esophagus | ESCC | 4.83e-03 | 5.83e-02 | 0.1149 |
220074 | LRTOMT | P16T-E | Human | Esophagus | ESCC | 2.80e-12 | 1.86e-01 | 0.1153 |
220074 | LRTOMT | P20T-E | Human | Esophagus | ESCC | 6.31e-09 | 2.40e-01 | 0.1124 |
220074 | LRTOMT | P21T-E | Human | Esophagus | ESCC | 9.92e-11 | 2.27e-01 | 0.1617 |
220074 | LRTOMT | P22T-E | Human | Esophagus | ESCC | 7.89e-03 | 7.88e-02 | 0.1236 |
220074 | LRTOMT | P23T-E | Human | Esophagus | ESCC | 1.02e-27 | 7.23e-01 | 0.108 |
220074 | LRTOMT | P26T-E | Human | Esophagus | ESCC | 8.19e-05 | 1.09e-01 | 0.1276 |
220074 | LRTOMT | P27T-E | Human | Esophagus | ESCC | 1.10e-02 | 9.56e-02 | 0.1055 |
220074 | LRTOMT | P28T-E | Human | Esophagus | ESCC | 2.36e-07 | 1.53e-01 | 0.1149 |
220074 | LRTOMT | P30T-E | Human | Esophagus | ESCC | 8.33e-03 | 1.65e-01 | 0.137 |
220074 | LRTOMT | P31T-E | Human | Esophagus | ESCC | 5.48e-03 | 9.56e-02 | 0.1251 |
220074 | LRTOMT | P32T-E | Human | Esophagus | ESCC | 1.69e-02 | 1.24e-01 | 0.1666 |
220074 | LRTOMT | P39T-E | Human | Esophagus | ESCC | 2.63e-09 | 1.68e-01 | 0.0894 |
220074 | LRTOMT | P44T-E | Human | Esophagus | ESCC | 5.09e-07 | 1.37e-01 | 0.1096 |
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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 |
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 |
GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
GO:000854410 | Esophagus | ESCC | epidermis development | 193/8552 | 324/18723 | 2.87e-07 | 4.19e-06 | 193 |
GO:000206420 | Esophagus | ESCC | epithelial cell development | 136/8552 | 220/18723 | 9.50e-07 | 1.21e-05 | 136 |
GO:000991310 | Esophagus | ESCC | epidermal cell differentiation | 122/8552 | 202/18723 | 1.69e-05 | 1.51e-04 | 122 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
LRTOMT | SNV | Missense_Mutation | rs200149461 | c.380T>G | p.Val127Gly | p.V127G | Q8WZ04 | protein_coding | deleterious(0.03) | possibly_damaging(0.773) | TCGA-A2-A0T2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | PD |
LRTOMT | SNV | Missense_Mutation | rs200149461 | c.380N>G | p.Val127Gly | p.V127G | Q8WZ04 | protein_coding | deleterious(0.03) | possibly_damaging(0.773) | TCGA-B6-A1KF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRTOMT | SNV | Missense_Mutation | rs772038038 | c.383N>G | p.Glu128Gly | p.E128G | Q8WZ04 | protein_coding | tolerated(0.29) | benign(0.233) | TCGA-E9-A1NF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
LRTOMT | insertion | Nonsense_Mutation | novel | c.658_659insAGCCTGGGTAACAAAGCAAGACCCCC | p.Cys220Ter | p.C220* | Q8WZ04 | protein_coding | TCGA-B6-A0IE-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
LRTOMT | SNV | Missense_Mutation | novel | c.277G>A | p.Gly93Ser | p.G93S | Q8WZ04 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
LRTOMT | SNV | Missense_Mutation | rs370168246 | c.754C>T | p.Arg252Cys | p.R252C | Q8WZ04 | protein_coding | deleterious(0.02) | probably_damaging(0.963) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRTOMT | SNV | Missense_Mutation | c.656N>A | p.Arg219Gln | p.R219Q | Q8WZ04 | protein_coding | tolerated(0.16) | possibly_damaging(0.51) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
LRTOMT | SNV | Missense_Mutation | c.23N>T | p.Arg8Ile | p.R8I | Q8WZ04 | protein_coding | tolerated_low_confidence(0.06) | benign(0.001) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
LRTOMT | SNV | Missense_Mutation | c.472N>T | p.Arg158Cys | p.R158C | Q8WZ04 | protein_coding | deleterious(0.04) | probably_damaging(0.949) | TCGA-QG-A5Z2-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
LRTOMT | SNV | Missense_Mutation | rs754759504 | c.755N>A | p.Arg252His | p.R252H | Q8WZ04 | protein_coding | tolerated(0.36) | benign(0.04) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <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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