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Gene: LSM5 |
Gene summary for LSM5 |
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Gene information | Species | Human | Gene symbol | LSM5 | Gene ID | 23658 |
Gene name | LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated | |
Gene Alias | YER146W | |
Cytomap | 7p14.3 | |
Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q9Y4Y9 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
23658 | LSM5 | SYSMH4 | Human | Oral cavity | OSCC | 9.87e-09 | 3.32e-01 | 0.1226 |
23658 | LSM5 | SYSMH5 | Human | Oral cavity | OSCC | 5.74e-14 | 7.86e-01 | 0.0647 |
23658 | LSM5 | SYSMH6 | Human | Oral cavity | OSCC | 4.31e-10 | 8.93e-01 | 0.1275 |
23658 | LSM5 | P4_S8_cSCC | Human | Skin | cSCC | 5.66e-13 | 1.46e-01 | -0.3095 |
23658 | LSM5 | P5_S10_cSCC | Human | Skin | cSCC | 2.10e-19 | 2.19e-01 | -0.299 |
23658 | LSM5 | P1_cSCC | Human | Skin | cSCC | 3.28e-39 | 1.71e+00 | 0.0292 |
23658 | LSM5 | P2_cSCC | Human | Skin | cSCC | 9.61e-38 | 1.29e+00 | -0.024 |
23658 | LSM5 | P4_cSCC | Human | Skin | cSCC | 5.46e-62 | 1.65e+00 | -0.00290000000000005 |
23658 | LSM5 | P10_cSCC | Human | Skin | cSCC | 1.00e-56 | 2.60e+00 | 0.1017 |
23658 | LSM5 | cSCC_p1 | Human | Skin | cSCC | 1.63e-11 | 4.00e-01 | -0.1916 |
23658 | LSM5 | cSCC_p10 | Human | Skin | cSCC | 2.93e-03 | 2.57e-01 | -0.2095 |
23658 | LSM5 | cSCC_p4 | Human | Skin | cSCC | 9.88e-18 | 4.07e-01 | -0.2022 |
23658 | LSM5 | cSCC_p6 | Human | Skin | cSCC | 9.56e-14 | 4.47e-01 | -0.1989 |
23658 | LSM5 | cSCC_p8 | Human | Skin | cSCC | 1.95e-12 | 2.93e-01 | -0.1971 |
23658 | LSM5 | cSCC_p9 | Human | Skin | cSCC | 2.32e-10 | 2.87e-01 | -0.1991 |
23658 | LSM5 | Adj_PTCwithHT_6 | Human | Thyroid | HT | 3.50e-02 | -3.53e-01 | 0.02 |
23658 | LSM5 | PTCwithHT_8 | Human | Thyroid | HT | 1.94e-02 | -3.12e-01 | 0.0351 |
23658 | LSM5 | PTCwithoutHT_2 | Human | Thyroid | PTC | 4.81e-03 | -3.47e-01 | 0.0419 |
23658 | LSM5 | male-WTA | Human | Thyroid | PTC | 2.19e-42 | -2.02e-01 | 0.1037 |
23658 | LSM5 | nodule-WTA | Human | Thyroid | goiters | 1.50e-02 | -4.20e-01 | 0.0534 |
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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: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: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: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:000640113 | Breast | IDC | RNA catabolic process | 38/1434 | 278/18723 | 3.54e-04 | 5.16e-03 | 38 |
GO:000640213 | Breast | IDC | mRNA catabolic process | 33/1434 | 232/18723 | 4.12e-04 | 5.66e-03 | 33 |
GO:190136112 | Breast | IDC | organic cyclic compound catabolic process | 56/1434 | 495/18723 | 2.12e-03 | 1.99e-02 | 56 |
GO:004670012 | Breast | IDC | heterocycle catabolic process | 51/1434 | 445/18723 | 2.51e-03 | 2.25e-02 | 51 |
GO:003465513 | Breast | IDC | nucleobase-containing compound catabolic process | 47/1434 | 407/18723 | 3.12e-03 | 2.63e-02 | 47 |
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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 |
LSM5 | SNV | Missense_Mutation | rs376563041 | c.29N>T | p.Ser10Leu | p.S10L | Q9Y4Y9 | protein_coding | tolerated(0.07) | benign(0.007) | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD |
LSM5 | SNV | Missense_Mutation | c.90N>A | p.Met30Ile | p.M30I | Q9Y4Y9 | protein_coding | deleterious(0.02) | benign(0.428) | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
LSM5 | SNV | Missense_Mutation | rs376563041 | c.29C>T | p.Ser10Leu | p.S10L | Q9Y4Y9 | protein_coding | tolerated(0.07) | benign(0.007) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD |
LSM5 | SNV | Missense_Mutation | novel | c.125G>A | p.Gly42Glu | p.G42E | Q9Y4Y9 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LSM5 | SNV | Missense_Mutation | novel | c.116C>T | p.Thr39Ile | p.T39I | Q9Y4Y9 | protein_coding | tolerated(0.05) | benign(0.211) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
LSM5 | SNV | Missense_Mutation | c.74N>T | p.Arg25Ile | p.R25I | Q9Y4Y9 | protein_coding | deleterious(0) | probably_damaging(0.912) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
LSM5 | SNV | Missense_Mutation | novel | c.85G>A | p.Val29Met | p.V29M | Q9Y4Y9 | protein_coding | tolerated(0.06) | possibly_damaging(0.734) | TCGA-56-7730-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | unknown | PD |
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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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