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Gene: LSM4 |
Gene summary for LSM4 |
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Gene information | Species | Human | Gene symbol | LSM4 | Gene ID | 25804 |
Gene name | LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated | |
Gene Alias | GRP | |
Cytomap | 19p13.11 | |
Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | U3KQK1 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
25804 | LSM4 | P10T-E | Human | Esophagus | ESCC | 3.82e-96 | 2.00e+00 | 0.116 |
25804 | LSM4 | P11T-E | Human | Esophagus | ESCC | 2.46e-26 | 1.21e+00 | 0.1426 |
25804 | LSM4 | P12T-E | Human | Esophagus | ESCC | 7.06e-60 | 1.22e+00 | 0.1122 |
25804 | LSM4 | P15T-E | Human | Esophagus | ESCC | 4.68e-58 | 1.57e+00 | 0.1149 |
25804 | LSM4 | P16T-E | Human | Esophagus | ESCC | 8.52e-45 | 1.23e+00 | 0.1153 |
25804 | LSM4 | P17T-E | Human | Esophagus | ESCC | 1.08e-29 | 1.43e+00 | 0.1278 |
25804 | LSM4 | P19T-E | Human | Esophagus | ESCC | 4.15e-17 | 2.37e+00 | 0.1662 |
25804 | LSM4 | P20T-E | Human | Esophagus | ESCC | 1.06e-68 | 1.43e+00 | 0.1124 |
25804 | LSM4 | P21T-E | Human | Esophagus | ESCC | 7.88e-100 | 2.70e+00 | 0.1617 |
25804 | LSM4 | P22T-E | Human | Esophagus | ESCC | 1.44e-95 | 1.73e+00 | 0.1236 |
25804 | LSM4 | P23T-E | Human | Esophagus | ESCC | 5.12e-73 | 1.99e+00 | 0.108 |
25804 | LSM4 | P24T-E | Human | Esophagus | ESCC | 2.89e-85 | 1.90e+00 | 0.1287 |
25804 | LSM4 | P26T-E | Human | Esophagus | ESCC | 5.34e-85 | 1.91e+00 | 0.1276 |
25804 | LSM4 | P27T-E | Human | Esophagus | ESCC | 1.87e-63 | 1.56e+00 | 0.1055 |
25804 | LSM4 | P28T-E | Human | Esophagus | ESCC | 2.25e-94 | 2.11e+00 | 0.1149 |
25804 | LSM4 | P30T-E | Human | Esophagus | ESCC | 1.19e-29 | 1.51e+00 | 0.137 |
25804 | LSM4 | P31T-E | Human | Esophagus | ESCC | 3.57e-91 | 2.00e+00 | 0.1251 |
25804 | LSM4 | P32T-E | Human | Esophagus | ESCC | 7.81e-100 | 2.30e+00 | 0.1666 |
25804 | LSM4 | P36T-E | Human | Esophagus | ESCC | 3.59e-34 | 1.24e+00 | 0.1187 |
25804 | LSM4 | P37T-E | Human | Esophagus | ESCC | 2.22e-54 | 1.55e+00 | 0.1371 |
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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). |
Page: 1 2 3 4 5 6 7 8 9 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
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:00064028 | Breast | Precancer | mRNA catabolic process | 31/1080 | 232/18723 | 1.12e-05 | 2.93e-04 | 31 |
GO:00064018 | Breast | Precancer | RNA catabolic process | 34/1080 | 278/18723 | 2.88e-05 | 6.39e-04 | 34 |
GO:00346558 | Breast | Precancer | nucleobase-containing compound catabolic process | 42/1080 | 407/18723 | 1.91e-04 | 3.06e-03 | 42 |
GO:00467007 | Breast | Precancer | heterocycle catabolic process | 44/1080 | 445/18723 | 3.49e-04 | 4.88e-03 | 44 |
GO:00442708 | Breast | Precancer | cellular nitrogen compound catabolic process | 44/1080 | 451/18723 | 4.64e-04 | 6.12e-03 | 44 |
GO:00003873 | Breast | Precancer | spliceosomal snRNP assembly | 10/1080 | 50/18723 | 4.86e-04 | 6.35e-03 | 10 |
GO:00009566 | Breast | Precancer | nuclear-transcribed mRNA catabolic process | 16/1080 | 112/18723 | 6.87e-04 | 8.36e-03 | 16 |
GO:00194397 | Breast | Precancer | aromatic compound catabolic process | 44/1080 | 467/18723 | 9.55e-04 | 1.07e-02 | 44 |
GO:19013617 | Breast | Precancer | organic cyclic compound catabolic process | 45/1080 | 495/18723 | 1.73e-03 | 1.74e-02 | 45 |
GO:002261314 | Breast | IDC | ribonucleoprotein complex biogenesis | 83/1434 | 463/18723 | 2.01e-13 | 5.20e-11 | 83 |
GO:007182614 | Breast | IDC | ribonucleoprotein complex subunit organization | 52/1434 | 227/18723 | 5.18e-13 | 1.21e-10 | 52 |
GO:002261814 | Breast | IDC | ribonucleoprotein complex assembly | 51/1434 | 220/18723 | 5.32e-13 | 1.21e-10 | 51 |
GO:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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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 |
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 |
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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 |
LSM4 | SNV | Missense_Mutation | c.137C>T | p.Thr46Met | p.T46M | Q9Y4Z0 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-AR-A0TS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
LSM4 | SNV | Missense_Mutation | rs764476513 | c.172G>A | p.Glu58Lys | p.E58K | Q9Y4Z0 | protein_coding | deleterious(0.01) | possibly_damaging(0.545) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LSM4 | SNV | Missense_Mutation | c.169C>T | p.Pro57Ser | p.P57S | Q9Y4Z0 | protein_coding | tolerated(0.13) | benign(0.055) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
LSM4 | SNV | Missense_Mutation | rs781537682 | c.164G>A | p.Arg55Gln | p.R55Q | Q9Y4Z0 | protein_coding | deleterious(0.01) | benign(0.183) | TCGA-AJ-A8CT-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LSM4 | SNV | Missense_Mutation | rs780420380 | c.217N>A | p.Asp73Asn | p.D73N | Q9Y4Z0 | protein_coding | tolerated(0.07) | benign(0.151) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LSM4 | SNV | Missense_Mutation | novel | c.319N>A | p.Ala107Thr | p.A107T | Q9Y4Z0 | protein_coding | tolerated(0.11) | benign(0.001) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
LSM4 | SNV | Missense_Mutation | c.208C>T | p.Arg70Cys | p.R70C | Q9Y4Z0 | protein_coding | deleterious(0.02) | possibly_damaging(0.502) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LSM4 | SNV | Missense_Mutation | novel | c.253G>C | p.Ala85Pro | p.A85P | Q9Y4Z0 | protein_coding | tolerated(0.07) | benign(0.43) | TCGA-DI-A1NO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
LSM4 | SNV | Missense_Mutation | c.8N>T | p.Pro3Leu | p.P3L | Q9Y4Z0 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-18-3409-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
LSM4 | SNV | Missense_Mutation | c.159N>G | p.Phe53Leu | p.F53L | Q9Y4Z0 | protein_coding | deleterious(0.01) | possibly_damaging(0.477) | TCGA-34-5929-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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