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Gene: LSM2 |
Gene summary for LSM2 |
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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 |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
57819 | LSM2 | EEC-subject1 | Human | Endometrium | EEC | 2.42e-09 | -2.57e-01 | -0.2682 |
57819 | LSM2 | EEC-subject2 | Human | Endometrium | EEC | 1.35e-14 | -3.56e-01 | -0.2607 |
57819 | LSM2 | EEC-subject3 | Human | Endometrium | EEC | 9.55e-35 | -4.18e-01 | -0.2525 |
57819 | LSM2 | EEC-subject4 | Human | Endometrium | EEC | 3.55e-10 | -2.46e-01 | -0.2571 |
57819 | LSM2 | EEC-subject5 | Human | Endometrium | EEC | 6.13e-04 | -1.32e-01 | -0.249 |
57819 | LSM2 | GSM5276934 | Human | Endometrium | EEC | 2.99e-19 | -4.26e-01 | -0.0913 |
57819 | LSM2 | GSM5276937 | Human | Endometrium | EEC | 7.82e-10 | -3.52e-01 | -0.0897 |
57819 | LSM2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 7.63e-31 | -3.49e-01 | -0.1869 |
57819 | LSM2 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 4.70e-21 | -4.10e-01 | -0.1875 |
57819 | LSM2 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 6.27e-32 | -3.35e-01 | -0.1883 |
57819 | LSM2 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 3.09e-36 | -3.15e-01 | -0.1934 |
57819 | LSM2 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 6.75e-42 | -2.12e-01 | -0.1917 |
57819 | LSM2 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 1.51e-35 | -2.80e-01 | -0.1916 |
57819 | LSM2 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 7.28e-05 | 1.25e-02 | -0.1269 |
57819 | LSM2 | LZE2T | Human | Esophagus | ESCC | 2.41e-03 | 9.11e-01 | 0.082 |
57819 | LSM2 | LZE4T | Human | Esophagus | ESCC | 3.75e-27 | 8.40e-01 | 0.0811 |
57819 | LSM2 | LZE5T | Human | Esophagus | ESCC | 5.00e-05 | 7.05e-01 | 0.0514 |
57819 | LSM2 | LZE7T | Human | Esophagus | ESCC | 1.22e-15 | 1.26e+00 | 0.0667 |
57819 | LSM2 | LZE8T | Human | Esophagus | ESCC | 5.40e-13 | 6.08e-01 | 0.067 |
57819 | LSM2 | LZE20T | Human | Esophagus | ESCC | 6.52e-13 | 5.68e-01 | 0.0662 |
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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: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 |
GO:000037514 | Breast | IDC | RNA splicing, via transesterification reactions | 58/1434 | 324/18723 | 9.44e-10 | 9.58e-08 | 58 |
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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 |
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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 |
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 |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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