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Gene: LSM3 |
Gene summary for LSM3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LSM3 | Gene ID | 27258 |
| Gene name | LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated | |
| Gene Alias | SMX4 | |
| Cytomap | 3p25.1 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | P62310 |
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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 |
| 27258 | LSM3 | GSM4909281 | Human | Breast | IDC | 1.00e-16 | 5.55e-01 | 0.21 |
| 27258 | LSM3 | GSM4909285 | Human | Breast | IDC | 1.40e-10 | 4.98e-01 | 0.21 |
| 27258 | LSM3 | GSM4909286 | Human | Breast | IDC | 2.74e-02 | 1.91e-01 | 0.1081 |
| 27258 | LSM3 | GSM4909288 | Human | Breast | IDC | 1.36e-02 | 3.19e-01 | 0.0988 |
| 27258 | LSM3 | GSM4909290 | Human | Breast | IDC | 6.02e-17 | 6.16e-01 | 0.2096 |
| 27258 | LSM3 | GSM4909293 | Human | Breast | IDC | 1.13e-17 | 5.52e-01 | 0.1581 |
| 27258 | LSM3 | GSM4909294 | Human | Breast | IDC | 2.11e-19 | 4.75e-01 | 0.2022 |
| 27258 | LSM3 | GSM4909296 | Human | Breast | IDC | 4.99e-09 | -1.93e-02 | 0.1524 |
| 27258 | LSM3 | GSM4909297 | Human | Breast | IDC | 9.59e-16 | 3.05e-02 | 0.1517 |
| 27258 | LSM3 | GSM4909298 | Human | Breast | IDC | 1.44e-04 | 3.96e-01 | 0.1551 |
| 27258 | LSM3 | GSM4909301 | Human | Breast | IDC | 1.89e-06 | 3.00e-01 | 0.1577 |
| 27258 | LSM3 | GSM4909308 | Human | Breast | IDC | 6.22e-08 | 3.86e-01 | 0.158 |
| 27258 | LSM3 | GSM4909311 | Human | Breast | IDC | 2.22e-34 | -2.02e-01 | 0.1534 |
| 27258 | LSM3 | GSM4909312 | Human | Breast | IDC | 8.43e-12 | -3.42e-02 | 0.1552 |
| 27258 | LSM3 | GSM4909315 | Human | Breast | IDC | 9.65e-55 | 9.54e-01 | 0.21 |
| 27258 | LSM3 | GSM4909316 | Human | Breast | IDC | 1.85e-25 | 8.27e-01 | 0.21 |
| 27258 | LSM3 | GSM4909317 | Human | Breast | IDC | 3.81e-06 | 3.71e-01 | 0.1355 |
| 27258 | LSM3 | GSM4909318 | Human | Breast | IDC | 1.88e-12 | 7.44e-01 | 0.2031 |
| 27258 | LSM3 | GSM4909319 | Human | Breast | IDC | 4.14e-40 | -1.38e-01 | 0.1563 |
| 27258 | LSM3 | GSM4909320 | Human | Breast | IDC | 2.20e-04 | 7.53e-02 | 0.1575 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
| GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
| GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
| GO:000037514 | Breast | IDC | RNA splicing, via transesterification reactions | 58/1434 | 324/18723 | 9.44e-10 | 9.58e-08 | 58 |
| GO:000037714 | Breast | IDC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:000039814 | Breast | IDC | mRNA splicing, via spliceosome | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:000838024 | Breast | DCIS | RNA splicing | 73/1390 | 434/18723 | 3.05e-11 | 5.08e-09 | 73 |
| GO:000037524 | Breast | DCIS | RNA splicing, via transesterification reactions | 58/1390 | 324/18723 | 2.89e-10 | 3.34e-08 | 58 |
| GO:000037724 | Breast | DCIS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1390 | 320/18723 | 5.01e-10 | 5.35e-08 | 57 |
| GO:000039824 | Breast | DCIS | mRNA splicing, via spliceosome | 57/1390 | 320/18723 | 5.01e-10 | 5.35e-08 | 57 |
| GO:000838010 | Cervix | CC | RNA splicing | 76/2311 | 434/18723 | 9.79e-04 | 8.19e-03 | 76 |
| GO:000037710 | Cervix | CC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000039810 | Cervix | CC | mRNA splicing, via spliceosome | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000037510 | Cervix | CC | RNA splicing, via transesterification reactions | 55/2311 | 324/18723 | 8.61e-03 | 4.44e-02 | 55 |
| GO:00339626 | Cervix | CC | P-body assembly | 7/2311 | 21/18723 | 1.04e-02 | 4.97e-02 | 7 |
| GO:000838015 | Cervix | N_HPV | RNA splicing | 23/534 | 434/18723 | 3.44e-03 | 2.80e-02 | 23 |
| GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
| GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa030408 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
| hsa030186 | Breast | Precancer | RNA degradation | 14/684 | 79/8465 | 3.97e-03 | 2.37e-02 | 1.81e-02 | 14 |
| hsa0304013 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
| hsa0301811 | Breast | Precancer | RNA degradation | 14/684 | 79/8465 | 3.97e-03 | 2.37e-02 | 1.81e-02 | 14 |
| 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 |
| 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 |
| Page: 1 2 3 |
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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 |
| LSM3 | SNV | Missense_Mutation | novel | c.193N>A | p.Glu65Lys | p.E65K | P62310 | protein_coding | deleterious(0.01) | probably_damaging(0.955) | TCGA-Q1-A5R1-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LSM3 | SNV | Missense_Mutation | c.122N>A | p.Gly41Asp | p.G41D | P62310 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LSM3 | SNV | Missense_Mutation | rs776138749 | c.283N>A | p.Val95Ile | p.V95I | P62310 | protein_coding | tolerated(0.51) | benign(0.122) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LSM3 | SNV | Missense_Mutation | novel | c.179C>A | p.Thr60Asn | p.T60N | P62310 | protein_coding | deleterious(0.01) | probably_damaging(0.952) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| LSM3 | SNV | Missense_Mutation | novel | c.107N>T | p.Asp36Val | p.D36V | P62310 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-55-6982-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | gemzar | PD |
| LSM3 | SNV | Missense_Mutation | novel | c.259G>A | p.Val87Ile | p.V87I | P62310 | protein_coding | tolerated(0.15) | benign(0.029) | TCGA-85-A50M-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| LSM3 | SNV | Missense_Mutation | novel | c.143N>G | p.Gln48Arg | p.Q48R | P62310 | protein_coding | tolerated(0.06) | probably_damaging(0.967) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
| LSM3 | SNV | Missense_Mutation | c.31N>G | p.Thr11Ala | p.T11A | P62310 | protein_coding | tolerated(0.42) | benign(0) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR | |
| LSM3 | SNV | Missense_Mutation | novel | c.253N>A | p.Leu85Ile | p.L85I | P62310 | protein_coding | tolerated(0.08) | possibly_damaging(0.764) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response |
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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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