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Gene: LSM2 |
Gene summary for LSM2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LSM2 | Gene ID | 57819 |
| Gene name | LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated | |
| Gene Alias | C6orf28 | |
| Cytomap | 6p21.33 | |
| Gene Type | protein-coding | GO ID | GO:0000244 | UniProtAcc | Q9Y333 |
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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 |
| 57819 | LSM2 | GSM4909281 | Human | Breast | IDC | 5.07e-13 | 5.11e-01 | 0.21 |
| 57819 | LSM2 | GSM4909282 | Human | Breast | IDC | 2.96e-25 | 6.09e-01 | -0.0288 |
| 57819 | LSM2 | GSM4909285 | Human | Breast | IDC | 1.30e-12 | 4.22e-01 | 0.21 |
| 57819 | LSM2 | GSM4909286 | Human | Breast | IDC | 4.95e-04 | 2.07e-01 | 0.1081 |
| 57819 | LSM2 | GSM4909293 | Human | Breast | IDC | 1.58e-02 | 2.92e-01 | 0.1581 |
| 57819 | LSM2 | GSM4909296 | Human | Breast | IDC | 1.28e-05 | 8.16e-02 | 0.1524 |
| 57819 | LSM2 | GSM4909297 | Human | Breast | IDC | 3.70e-09 | -1.87e-02 | 0.1517 |
| 57819 | LSM2 | GSM4909307 | Human | Breast | IDC | 2.96e-02 | 2.96e-01 | 0.1569 |
| 57819 | LSM2 | GSM4909308 | Human | Breast | IDC | 1.60e-04 | 3.84e-01 | 0.158 |
| 57819 | LSM2 | GSM4909311 | Human | Breast | IDC | 1.00e-28 | -1.78e-01 | 0.1534 |
| 57819 | LSM2 | GSM4909312 | Human | Breast | IDC | 1.79e-12 | 1.73e-01 | 0.1552 |
| 57819 | LSM2 | GSM4909315 | Human | Breast | IDC | 3.45e-02 | 2.47e-01 | 0.21 |
| 57819 | LSM2 | GSM4909316 | Human | Breast | IDC | 2.84e-02 | 1.77e-01 | 0.21 |
| 57819 | LSM2 | GSM4909318 | Human | Breast | IDC | 6.57e-03 | 4.59e-01 | 0.2031 |
| 57819 | LSM2 | GSM4909319 | Human | Breast | IDC | 7.16e-36 | -6.26e-02 | 0.1563 |
| 57819 | LSM2 | GSM4909320 | Human | Breast | IDC | 2.00e-03 | -7.33e-02 | 0.1575 |
| 57819 | LSM2 | GSM4909321 | Human | Breast | IDC | 2.55e-08 | -5.33e-02 | 0.1559 |
| 57819 | LSM2 | brca10 | Human | Breast | Precancer | 1.45e-06 | -2.86e-01 | -0.0029 |
| 57819 | LSM2 | M2 | Human | Breast | IDC | 3.21e-04 | 2.46e-01 | 0.21 |
| 57819 | LSM2 | NCCBC14 | Human | Breast | DCIS | 7.40e-06 | -1.82e-01 | 0.2021 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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). |
| 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 |
| GO:000640227 | Thyroid | ATC | mRNA catabolic process | 140/6293 | 232/18723 | 5.08e-17 | 4.65e-15 | 140 |
| GO:003465525 | Thyroid | ATC | nucleobase-containing compound catabolic process | 217/6293 | 407/18723 | 1.20e-16 | 1.04e-14 | 217 |
| GO:004670024 | Thyroid | ATC | heterocycle catabolic process | 228/6293 | 445/18723 | 7.26e-15 | 4.50e-13 | 228 |
| GO:007182635 | Thyroid | ATC | ribonucleoprotein complex subunit organization | 133/6293 | 227/18723 | 8.32e-15 | 5.01e-13 | 133 |
| GO:002261835 | Thyroid | ATC | ribonucleoprotein complex assembly | 129/6293 | 220/18723 | 1.93e-14 | 1.10e-12 | 129 |
| GO:004427025 | Thyroid | ATC | cellular nitrogen compound catabolic process | 229/6293 | 451/18723 | 2.25e-14 | 1.27e-12 | 229 |
| GO:001943924 | Thyroid | ATC | aromatic compound catabolic process | 232/6293 | 467/18723 | 3.05e-13 | 1.44e-11 | 232 |
| GO:190136124 | Thyroid | ATC | organic cyclic compound catabolic process | 238/6293 | 495/18723 | 1.12e-11 | 4.12e-10 | 238 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0304023 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
| hsa0301821 | Breast | IDC | RNA degradation | 16/867 | 79/8465 | 5.65e-03 | 3.13e-02 | 2.34e-02 | 16 |
| hsa0304033 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
| hsa0301831 | Breast | IDC | RNA degradation | 16/867 | 79/8465 | 5.65e-03 | 3.13e-02 | 2.34e-02 | 16 |
| hsa0304043 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
| hsa030184 | Breast | DCIS | RNA degradation | 16/846 | 79/8465 | 4.45e-03 | 2.46e-02 | 1.82e-02 | 16 |
| hsa0304053 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
| hsa030185 | Breast | DCIS | RNA degradation | 16/846 | 79/8465 | 4.45e-03 | 2.46e-02 | 1.82e-02 | 16 |
| hsa03040 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030401 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030402 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030403 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030404 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
| hsa030405 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
| hsa030409 | Endometrium | AEH | Spliceosome | 54/1197 | 217/8465 | 1.47e-05 | 1.65e-04 | 1.21e-04 | 54 |
| hsa0304014 | Endometrium | AEH | Spliceosome | 54/1197 | 217/8465 | 1.47e-05 | 1.65e-04 | 1.21e-04 | 54 |
| hsa0304024 | Endometrium | EEC | Spliceosome | 54/1237 | 217/8465 | 3.78e-05 | 3.88e-04 | 2.89e-04 | 54 |
| hsa030187 | Endometrium | EEC | RNA degradation | 20/1237 | 79/8465 | 8.36e-03 | 3.88e-02 | 2.89e-02 | 20 |
| hsa0304034 | Endometrium | EEC | Spliceosome | 54/1237 | 217/8465 | 3.78e-05 | 3.88e-04 | 2.89e-04 | 54 |
| hsa0301812 | Endometrium | EEC | RNA degradation | 20/1237 | 79/8465 | 8.36e-03 | 3.88e-02 | 2.89e-02 | 20 |
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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 |
| LSM2 | SNV | Missense_Mutation | novel | c.232N>A | p.Asp78Asn | p.D78N | Q9Y333 | protein_coding | tolerated(0.06) | benign(0.086) | TCGA-PL-A8LZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| LSM2 | SNV | Missense_Mutation | c.4N>G | p.Leu2Val | p.L2V | Q9Y333 | protein_coding | deleterious(0.01) | possibly_damaging(0.762) | TCGA-AG-3893-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folinic | CR | |
| LSM2 | SNV | Missense_Mutation | novel | c.147G>T | p.Glu49Asp | p.E49D | Q9Y333 | protein_coding | tolerated(0.44) | benign(0.001) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| LSM2 | SNV | Missense_Mutation | novel | c.17N>G | p.Phe6Cys | p.F6C | Q9Y333 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-DF-A2KV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LSM2 | SNV | Missense_Mutation | novel | c.167N>T | p.Ser56Leu | p.S56L | Q9Y333 | protein_coding | tolerated(0.08) | possibly_damaging(0.833) | TCGA-CV-7104-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LSM2 | SNV | Missense_Mutation | novel | c.256N>T | p.Ala86Ser | p.A86S | Q9Y333 | protein_coding | tolerated(0.4) | benign(0.003) | TCGA-HU-A4HB-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | ts-1 | PD |
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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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