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Gene: LYSMD2 |
Gene summary for LYSMD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LYSMD2 | Gene ID | 256586 |
| Gene name | LysM domain containing 2 | |
| Gene Alias | LYSMD2 | |
| Cytomap | 15q21.2 | |
| Gene Type | protein-coding | GO ID | NA | UniProtAcc | Q8IV50 |
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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 |
| 256586 | LYSMD2 | LZE4T | Human | Esophagus | ESCC | 2.28e-02 | 3.12e-02 | 0.0811 |
| 256586 | LYSMD2 | LZE22T | Human | Esophagus | ESCC | 6.28e-04 | 3.21e-01 | 0.068 |
| 256586 | LYSMD2 | LZE24T | Human | Esophagus | ESCC | 6.69e-14 | 3.41e-01 | 0.0596 |
| 256586 | LYSMD2 | P1T-E | Human | Esophagus | ESCC | 8.08e-05 | 2.09e-01 | 0.0875 |
| 256586 | LYSMD2 | P2T-E | Human | Esophagus | ESCC | 1.96e-15 | 2.02e-01 | 0.1177 |
| 256586 | LYSMD2 | P4T-E | Human | Esophagus | ESCC | 1.91e-29 | 6.91e-01 | 0.1323 |
| 256586 | LYSMD2 | P5T-E | Human | Esophagus | ESCC | 9.46e-18 | 4.49e-01 | 0.1327 |
| 256586 | LYSMD2 | P8T-E | Human | Esophagus | ESCC | 7.85e-14 | 3.80e-01 | 0.0889 |
| 256586 | LYSMD2 | P9T-E | Human | Esophagus | ESCC | 2.87e-32 | 8.51e-01 | 0.1131 |
| 256586 | LYSMD2 | P10T-E | Human | Esophagus | ESCC | 9.46e-13 | 3.53e-01 | 0.116 |
| 256586 | LYSMD2 | P11T-E | Human | Esophagus | ESCC | 3.62e-12 | 4.22e-01 | 0.1426 |
| 256586 | LYSMD2 | P12T-E | Human | Esophagus | ESCC | 1.37e-16 | 4.28e-01 | 0.1122 |
| 256586 | LYSMD2 | P15T-E | Human | Esophagus | ESCC | 1.14e-16 | 3.99e-01 | 0.1149 |
| 256586 | LYSMD2 | P16T-E | Human | Esophagus | ESCC | 1.91e-20 | 5.07e-01 | 0.1153 |
| 256586 | LYSMD2 | P19T-E | Human | Esophagus | ESCC | 2.38e-11 | 5.55e-01 | 0.1662 |
| 256586 | LYSMD2 | P20T-E | Human | Esophagus | ESCC | 3.11e-23 | 4.79e-01 | 0.1124 |
| 256586 | LYSMD2 | P21T-E | Human | Esophagus | ESCC | 5.80e-09 | 3.07e-01 | 0.1617 |
| 256586 | LYSMD2 | P22T-E | Human | Esophagus | ESCC | 8.31e-21 | 3.42e-01 | 0.1236 |
| 256586 | LYSMD2 | P23T-E | Human | Esophagus | ESCC | 2.24e-26 | 7.47e-01 | 0.108 |
| 256586 | LYSMD2 | P24T-E | Human | Esophagus | ESCC | 1.25e-16 | 4.23e-01 | 0.1287 |
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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 | ||
| 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 |
| ∗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 |
| LYSMD2 | SNV | Missense_Mutation | c.323N>G | p.Phe108Cys | p.F108C | Q8IV50 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LYSMD2 | SNV | Missense_Mutation | c.466N>T | p.Leu156Phe | p.L156F | Q8IV50 | protein_coding | tolerated(0.71) | benign(0.001) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| LYSMD2 | SNV | Missense_Mutation | c.394N>A | p.Asp132Asn | p.D132N | Q8IV50 | protein_coding | deleterious(0.01) | possibly_damaging(0.797) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LYSMD2 | SNV | Missense_Mutation | novel | c.535N>G | p.Phe179Val | p.F179V | Q8IV50 | protein_coding | deleterious(0) | probably_damaging(0.957) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| LYSMD2 | SNV | Missense_Mutation | novel | c.339N>T | p.Leu113Phe | p.L113F | Q8IV50 | protein_coding | deleterious(0.01) | possibly_damaging(0.838) | TCGA-BS-A0TC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LYSMD2 | SNV | Missense_Mutation | novel | c.330N>T | p.Lys110Asn | p.K110N | Q8IV50 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-D1-A16X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LYSMD2 | SNV | Missense_Mutation | c.415N>C | p.Ala139Pro | p.A139P | Q8IV50 | protein_coding | tolerated(0.27) | benign(0.006) | TCGA-53-7624-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
| LYSMD2 | SNV | Missense_Mutation | c.389N>G | p.Ser130Cys | p.S130C | Q8IV50 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-55-A4DF-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| LYSMD2 | SNV | Missense_Mutation | c.368N>C | p.Leu123Ser | p.L123S | Q8IV50 | protein_coding | tolerated(0.49) | benign(0.001) | TCGA-67-3771-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LYSMD2 | SNV | Missense_Mutation | novel | c.580N>A | p.Ala194Thr | p.A194T | Q8IV50 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-MP-A4T7-01 | Lung | lung 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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