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Gene: LSM12 |
Gene summary for LSM12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LSM12 | Gene ID | 124801 |
| Gene name | LSM12 homolog | |
| Gene Alias | PNAS-135 | |
| Cytomap | 17q21.31 | |
| Gene Type | protein-coding | GO ID | GO:0003674 | UniProtAcc | Q3MHD2 |
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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 |
| 124801 | LSM12 | LZE2D | Human | Esophagus | HGIN | 1.57e-04 | 4.21e-01 | 0.0642 |
| 124801 | LSM12 | LZE2T | Human | Esophagus | ESCC | 9.54e-06 | 5.50e-01 | 0.082 |
| 124801 | LSM12 | LZE4T | Human | Esophagus | ESCC | 4.82e-28 | 6.90e-01 | 0.0811 |
| 124801 | LSM12 | LZE5T | Human | Esophagus | ESCC | 1.40e-06 | 4.29e-01 | 0.0514 |
| 124801 | LSM12 | LZE7T | Human | Esophagus | ESCC | 3.42e-17 | 7.13e-01 | 0.0667 |
| 124801 | LSM12 | LZE8T | Human | Esophagus | ESCC | 5.66e-07 | 2.85e-01 | 0.067 |
| 124801 | LSM12 | LZE20T | Human | Esophagus | ESCC | 1.97e-04 | 1.75e-01 | 0.0662 |
| 124801 | LSM12 | LZE22D1 | Human | Esophagus | HGIN | 5.14e-03 | 1.70e-01 | 0.0595 |
| 124801 | LSM12 | LZE22T | Human | Esophagus | ESCC | 1.00e-09 | 5.03e-01 | 0.068 |
| 124801 | LSM12 | LZE24T | Human | Esophagus | ESCC | 5.18e-34 | 6.87e-01 | 0.0596 |
| 124801 | LSM12 | LZE21T | Human | Esophagus | ESCC | 1.57e-07 | 4.97e-01 | 0.0655 |
| 124801 | LSM12 | LZE6T | Human | Esophagus | ESCC | 3.41e-18 | 6.15e-01 | 0.0845 |
| 124801 | LSM12 | P1T-E | Human | Esophagus | ESCC | 1.88e-22 | 7.38e-01 | 0.0875 |
| 124801 | LSM12 | P2T-E | Human | Esophagus | ESCC | 1.30e-51 | 7.94e-01 | 0.1177 |
| 124801 | LSM12 | P4T-E | Human | Esophagus | ESCC | 7.71e-61 | 1.22e+00 | 0.1323 |
| 124801 | LSM12 | P5T-E | Human | Esophagus | ESCC | 1.88e-75 | 1.34e+00 | 0.1327 |
| 124801 | LSM12 | P8T-E | Human | Esophagus | ESCC | 6.40e-39 | 6.69e-01 | 0.0889 |
| 124801 | LSM12 | P9T-E | Human | Esophagus | ESCC | 8.50e-30 | 5.76e-01 | 0.1131 |
| 124801 | LSM12 | P10T-E | Human | Esophagus | ESCC | 1.09e-26 | 3.94e-01 | 0.116 |
| 124801 | LSM12 | P11T-E | Human | Esophagus | ESCC | 9.33e-27 | 7.76e-01 | 0.1426 |
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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 | ||
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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| 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 |
| LSM12 | SNV | Missense_Mutation | novel | c.433C>T | p.Pro145Ser | p.P145S | Q3MHD2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A2-A0T1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | herceptin | SD |
| LSM12 | insertion | In_Frame_Ins | novel | c.410_411insTGGGTTTTTCTTAGC | p.Met137delinsIleGlyPhePheLeuAla | p.M137delinsIGFFLA | Q3MHD2 | protein_coding | TCGA-AN-A0FS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LSM12 | deletion | Frame_Shift_Del | c.248delN | p.Asn83MetfsTer17 | p.N83Mfs*17 | Q3MHD2 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| LSM12 | SNV | Missense_Mutation | c.383A>C | p.Lys128Thr | p.K128T | Q3MHD2 | protein_coding | tolerated(0.95) | possibly_damaging(0.84) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| LSM12 | SNV | Missense_Mutation | novel | c.449N>G | p.Asn150Ser | p.N150S | Q3MHD2 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AG-A00Y-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| LSM12 | SNV | Missense_Mutation | novel | c.485N>C | p.Val162Ala | p.V162A | Q3MHD2 | protein_coding | deleterious(0) | benign(0.132) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LSM12 | SNV | Missense_Mutation | novel | c.295N>A | p.Leu99Met | p.L99M | Q3MHD2 | protein_coding | tolerated(0.06) | benign(0.243) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LSM12 | SNV | Missense_Mutation | c.403N>A | p.Val135Ile | p.V135I | Q3MHD2 | protein_coding | tolerated(0.46) | benign(0.003) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LSM12 | SNV | Missense_Mutation | c.59N>A | p.Cys20Tyr | p.C20Y | Q3MHD2 | protein_coding | deleterious(0.02) | probably_damaging(0.979) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LSM12 | SNV | Missense_Mutation | novel | c.212N>T | p.Asp71Val | p.D71V | Q3MHD2 | protein_coding | deleterious(0) | benign(0.207) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | 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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