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Gene: LSM1 |
Gene summary for LSM1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LSM1 | Gene ID | 27257 |
Gene name | LSM1 homolog, mRNA degradation associated | |
Gene Alias | CASM | |
Cytomap | 8p11.23 | |
Gene Type | protein-coding | GO ID | GO:0000288 | UniProtAcc | A0A0S2Z590 |
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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 |
27257 | LSM1 | GSM4909291 | Human | Breast | IDC | 6.32e-03 | 3.49e-01 | 0.1753 |
27257 | LSM1 | GSM4909296 | Human | Breast | IDC | 4.64e-04 | -6.91e-02 | 0.1524 |
27257 | LSM1 | GSM4909297 | Human | Breast | IDC | 6.30e-17 | 5.33e-01 | 0.1517 |
27257 | LSM1 | GSM4909308 | Human | Breast | IDC | 6.73e-04 | 3.05e-01 | 0.158 |
27257 | LSM1 | GSM4909309 | Human | Breast | IDC | 8.63e-13 | 5.17e-01 | 0.0483 |
27257 | LSM1 | GSM4909311 | Human | Breast | IDC | 7.79e-14 | -1.80e-01 | 0.1534 |
27257 | LSM1 | GSM4909312 | Human | Breast | IDC | 3.51e-06 | -1.30e-01 | 0.1552 |
27257 | LSM1 | GSM4909313 | Human | Breast | IDC | 1.46e-03 | -1.44e-01 | 0.0391 |
27257 | LSM1 | GSM4909317 | Human | Breast | IDC | 3.39e-16 | 5.37e-01 | 0.1355 |
27257 | LSM1 | GSM4909318 | Human | Breast | IDC | 6.17e-20 | 1.08e+00 | 0.2031 |
27257 | LSM1 | GSM4909319 | Human | Breast | IDC | 2.50e-19 | -6.03e-02 | 0.1563 |
27257 | LSM1 | GSM4909321 | Human | Breast | IDC | 6.95e-07 | -7.68e-02 | 0.1559 |
27257 | LSM1 | brca1 | Human | Breast | Precancer | 1.82e-03 | 3.27e-01 | -0.0338 |
27257 | LSM1 | NCCBC14 | Human | Breast | DCIS | 1.15e-02 | 6.47e-02 | 0.2021 |
27257 | LSM1 | NCCBC2 | Human | Breast | DCIS | 1.12e-06 | 4.76e-01 | 0.1554 |
27257 | LSM1 | NCCBC5 | Human | Breast | DCIS | 1.12e-04 | 1.01e-03 | 0.2046 |
27257 | LSM1 | P1 | Human | Breast | IDC | 1.80e-08 | -2.00e-01 | 0.1527 |
27257 | LSM1 | P2 | Human | Breast | IDC | 1.25e-26 | 8.66e-01 | 0.21 |
27257 | LSM1 | DCIS2 | Human | Breast | DCIS | 2.87e-35 | 8.78e-02 | 0.0085 |
27257 | LSM1 | LZE2T | Human | Esophagus | ESCC | 1.28e-03 | 8.37e-01 | 0.082 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000705216 | Thyroid | PTC | mitotic spindle organization | 64/5968 | 120/18723 | 8.69e-07 | 1.32e-05 | 64 |
GO:00000829 | Thyroid | PTC | G1/S transition of mitotic cell cycle | 102/5968 | 214/18723 | 9.48e-07 | 1.43e-05 | 102 |
GO:00448439 | Thyroid | PTC | cell cycle G1/S phase transition | 112/5968 | 241/18723 | 1.37e-06 | 1.96e-05 | 112 |
GO:19019878 | Thyroid | PTC | regulation of cell cycle phase transition | 167/5968 | 390/18723 | 2.97e-06 | 3.87e-05 | 167 |
GO:003424916 | Thyroid | PTC | negative regulation of cellular amide metabolic process | 122/5968 | 273/18723 | 5.50e-06 | 6.64e-05 | 122 |
GO:00343408 | Thyroid | PTC | response to type I interferon | 35/5968 | 58/18723 | 7.35e-06 | 8.60e-05 | 35 |
GO:00395286 | Thyroid | PTC | cytoplasmic pattern recognition receptor signaling pathway in response to virus | 23/5968 | 34/18723 | 1.98e-05 | 2.01e-04 | 23 |
GO:000275310 | Thyroid | PTC | cytoplasmic pattern recognition receptor signaling pathway | 35/5968 | 60/18723 | 2.09e-05 | 2.09e-04 | 35 |
GO:001714815 | Thyroid | PTC | negative regulation of translation | 108/5968 | 245/18723 | 3.75e-05 | 3.48e-04 | 108 |
GO:00710442 | Thyroid | PTC | histone mRNA catabolic process | 10/5968 | 11/18723 | 8.42e-05 | 7.03e-04 | 10 |
GO:009006816 | Thyroid | PTC | positive regulation of cell cycle process | 103/5968 | 236/18723 | 9.03e-05 | 7.50e-04 | 103 |
GO:00713577 | Thyroid | PTC | cellular response to type I interferon | 30/5968 | 52/18723 | 1.06e-04 | 8.56e-04 | 30 |
GO:00603377 | Thyroid | PTC | type I interferon signaling pathway | 29/5968 | 50/18723 | 1.21e-04 | 9.66e-04 | 29 |
GO:000283114 | Thyroid | PTC | regulation of response to biotic stimulus | 136/5968 | 327/18723 | 1.22e-04 | 9.69e-04 | 136 |
GO:009872710 | Thyroid | PTC | maintenance of cell number | 63/5968 | 134/18723 | 1.73e-04 | 1.32e-03 | 63 |
GO:200004515 | Thyroid | PTC | regulation of G1/S transition of mitotic cell cycle | 66/5968 | 142/18723 | 1.86e-04 | 1.41e-03 | 66 |
GO:19028067 | Thyroid | PTC | regulation of cell cycle G1/S phase transition | 76/5968 | 168/18723 | 1.87e-04 | 1.41e-03 | 76 |
GO:00083342 | Thyroid | PTC | histone mRNA metabolic process | 13/5968 | 17/18723 | 2.05e-04 | 1.52e-03 | 13 |
GO:00395297 | Thyroid | PTC | RIG-I signaling pathway | 18/5968 | 27/18723 | 2.15e-04 | 1.59e-03 | 18 |
GO:005122514 | Thyroid | PTC | spindle assembly | 56/5968 | 117/18723 | 2.17e-04 | 1.60e-03 | 56 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa030186 | Breast | Precancer | RNA degradation | 14/684 | 79/8465 | 3.97e-03 | 2.37e-02 | 1.81e-02 | 14 |
hsa0301811 | Breast | Precancer | RNA degradation | 14/684 | 79/8465 | 3.97e-03 | 2.37e-02 | 1.81e-02 | 14 |
hsa0301821 | Breast | IDC | RNA degradation | 16/867 | 79/8465 | 5.65e-03 | 3.13e-02 | 2.34e-02 | 16 |
hsa0301831 | Breast | IDC | RNA degradation | 16/867 | 79/8465 | 5.65e-03 | 3.13e-02 | 2.34e-02 | 16 |
hsa030184 | Breast | DCIS | RNA degradation | 16/846 | 79/8465 | 4.45e-03 | 2.46e-02 | 1.82e-02 | 16 |
hsa030185 | Breast | DCIS | RNA degradation | 16/846 | 79/8465 | 4.45e-03 | 2.46e-02 | 1.82e-02 | 16 |
hsa0301810 | Esophagus | HGIN | RNA degradation | 27/1383 | 79/8465 | 7.73e-05 | 9.00e-04 | 7.15e-04 | 27 |
hsa0301815 | Esophagus | HGIN | RNA degradation | 27/1383 | 79/8465 | 7.73e-05 | 9.00e-04 | 7.15e-04 | 27 |
hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
hsa03018 | Liver | Cirrhotic | RNA degradation | 44/2530 | 79/8465 | 1.43e-06 | 1.65e-05 | 1.02e-05 | 44 |
hsa030181 | Liver | Cirrhotic | RNA degradation | 44/2530 | 79/8465 | 1.43e-06 | 1.65e-05 | 1.02e-05 | 44 |
hsa030182 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
hsa030183 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
hsa030189 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
hsa0301814 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
hsa0301823 | Oral cavity | LP | RNA degradation | 39/2418 | 79/8465 | 6.98e-05 | 4.38e-04 | 2.83e-04 | 39 |
hsa0301833 | Oral cavity | LP | RNA degradation | 39/2418 | 79/8465 | 6.98e-05 | 4.38e-04 | 2.83e-04 | 39 |
hsa030188 | Prostate | BPH | RNA degradation | 29/1718 | 79/8465 | 5.17e-04 | 2.67e-03 | 1.65e-03 | 29 |
hsa0301813 | Prostate | BPH | RNA degradation | 29/1718 | 79/8465 | 5.17e-04 | 2.67e-03 | 1.65e-03 | 29 |
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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 |
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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. |
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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 |
LSM1 | SNV | Missense_Mutation | novel | c.98N>A | p.Arg33Lys | p.R33K | O15116 | protein_coding | deleterious(0.04) | possibly_damaging(0.71) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LSM1 | SNV | Missense_Mutation | c.146N>A | p.Arg49His | p.R49H | O15116 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AA-3681-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
LSM1 | SNV | Missense_Mutation | c.364N>A | p.Leu122Ile | p.L122I | O15116 | protein_coding | tolerated(0.05) | benign(0.209) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
LSM1 | SNV | Missense_Mutation | c.176T>G | p.Ile59Ser | p.I59S | O15116 | protein_coding | deleterious(0) | possibly_damaging(0.791) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
LSM1 | deletion | Frame_Shift_Del | c.165delA | p.Lys55AsnfsTer20 | p.K55Nfs*20 | O15116 | protein_coding | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |||
LSM1 | SNV | Missense_Mutation | novel | c.238G>A | p.Glu80Lys | p.E80K | O15116 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
LSM1 | SNV | Missense_Mutation | novel | c.312N>T | p.Gln104His | p.Q104H | O15116 | protein_coding | deleterious(0.02) | benign(0.428) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
LSM1 | SNV | Missense_Mutation | novel | c.382N>A | p.Asp128Asn | p.D128N | O15116 | protein_coding | deleterious(0.02) | benign(0.006) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
LSM1 | SNV | Missense_Mutation | novel | c.145C>T | p.Arg49Cys | p.R49C | O15116 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AX-A1C5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | SD |
LSM1 | SNV | Missense_Mutation | c.263N>G | p.Gln88Arg | p.Q88R | O15116 | protein_coding | tolerated(0.3) | benign(0.001) | TCGA-D1-A17Q-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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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