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Gene: LSM3 |
Gene summary for LSM3 |
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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 |
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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 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000037534 | Thyroid | ATC | RNA splicing, via transesterification reactions | 200/6293 | 324/18723 | 1.75e-25 | 7.39e-23 | 200 |
GO:000037734 | Thyroid | ATC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 197/6293 | 320/18723 | 6.54e-25 | 2.18e-22 | 197 |
GO:000039834 | Thyroid | ATC | mRNA splicing, via spliceosome | 197/6293 | 320/18723 | 6.54e-25 | 2.18e-22 | 197 |
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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 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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