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Gene: LRRTM4 |
Gene summary for LRRTM4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRRTM4 | Gene ID | 80059 |
Gene name | leucine rich repeat transmembrane neuronal 4 | |
Gene Alias | LRRTM4 | |
Cytomap | 2p12 | |
Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | Q6ZT31 |
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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 |
80059 | LRRTM4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.26e-05 | 2.01e-01 | -0.0811 |
80059 | LRRTM4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.30e-04 | 1.83e-01 | -0.1207 |
80059 | LRRTM4 | HTA11_696_2000001011 | Human | Colorectum | AD | 5.05e-06 | 1.78e-01 | -0.1464 |
80059 | LRRTM4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.55e-04 | 1.86e-01 | -0.059 |
80059 | LRRTM4 | HTA11_6818_2000001011 | Human | Colorectum | AD | 1.08e-04 | 3.01e-01 | 0.0112 |
80059 | LRRTM4 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.74e-22 | 9.53e-01 | 0.281 |
80059 | LRRTM4 | HTA12-15-2 | Human | Pancreas | PDAC | 3.78e-09 | 7.15e-01 | 0.2315 |
80059 | LRRTM4 | HTA12-16-2 | Human | Pancreas | PDAC | 1.71e-02 | 7.10e-01 | 0.0535 |
80059 | LRRTM4 | HTA12-23-1 | Human | Pancreas | PDAC | 1.09e-21 | 1.57e+00 | 0.3405 |
80059 | LRRTM4 | HTA12-25-1 | Human | Pancreas | PDAC | 3.74e-18 | 1.21e+00 | 0.313 |
80059 | LRRTM4 | HTA12-26-1 | Human | Pancreas | PDAC | 1.16e-49 | 1.76e+00 | 0.3728 |
80059 | LRRTM4 | HTA12-29-1 | Human | Pancreas | PDAC | 2.20e-55 | 1.32e+00 | 0.3722 |
80059 | LRRTM4 | HTA12-30-1 | Human | Pancreas | PDAC | 5.66e-08 | 1.55e+00 | 0.3671 |
80059 | LRRTM4 | HTA12-32-1 | Human | Pancreas | PDAC | 5.46e-10 | 1.49e+00 | 0.3624 |
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Transcriptomic changes along malignancy continuum. |
∗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:0050808 | Colorectum | AD | synapse organization | 112/3918 | 426/18723 | 4.25e-03 | 2.92e-02 | 112 |
GO:00508082 | Colorectum | MSS | synapse organization | 101/3467 | 426/18723 | 3.96e-03 | 2.89e-02 | 101 |
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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 |
LRRTM4 | SNV | Missense_Mutation | rs758217801 | c.673N>T | p.His225Tyr | p.H225Y | protein_coding | deleterious(0.02) | possibly_damaging(0.656) | TCGA-A2-A0EM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
LRRTM4 | SNV | Missense_Mutation | novel | c.433N>C | p.Lys145Gln | p.K145Q | protein_coding | tolerated(0.82) | benign(0.214) | TCGA-A7-A4SF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR | |
LRRTM4 | SNV | Missense_Mutation | c.98N>A | p.Arg33Lys | p.R33K | protein_coding | tolerated(0.17) | benign(0.024) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
LRRTM4 | SNV | Missense_Mutation | novel | c.1550G>A | p.Cys517Tyr | p.C517Y | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A18U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
LRRTM4 | SNV | Missense_Mutation | novel | c.520C>T | p.Pro174Ser | p.P174S | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-BH-AB28-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | |
LRRTM4 | SNV | Missense_Mutation | novel | c.1417N>A | p.Glu473Lys | p.E473K | protein_coding | tolerated(0.37) | benign(0.031) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
LRRTM4 | SNV | Missense_Mutation | c.1243N>A | p.Glu415Lys | p.E415K | protein_coding | tolerated(0.2) | benign(0.301) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | ||
LRRTM4 | SNV | Missense_Mutation | c.214A>T | p.Asn72Tyr | p.N72Y | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-GI-A2C8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Adriamycin | SD | ||
LRRTM4 | insertion | Frame_Shift_Ins | novel | c.132_133insGATTGCGGAG | p.Ile45AspfsTer8 | p.I45Dfs*8 | protein_coding | TCGA-BH-A0HN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |||
LRRTM4 | deletion | Frame_Shift_Del | novel | c.1111delA | p.Arg371AspfsTer13 | p.R371Dfs*13 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | 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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