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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 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| 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:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
| GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
| GO:19033118 | Breast | Precancer | regulation of mRNA metabolic process | 38/1080 | 288/18723 | 1.63e-06 | 5.97e-05 | 38 |
| 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:00098969 | Breast | Precancer | positive regulation of catabolic process | 48/1080 | 492/18723 | 2.62e-04 | 3.84e-03 | 48 |
| GO:00313319 | Breast | Precancer | positive regulation of cellular catabolic process | 43/1080 | 427/18723 | 2.75e-04 | 4.00e-03 | 43 |
| 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: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:00434888 | Breast | Precancer | regulation of mRNA stability | 19/1080 | 158/18723 | 1.92e-03 | 1.86e-02 | 19 |
| GO:00610138 | Breast | Precancer | regulation of mRNA catabolic process | 19/1080 | 166/18723 | 3.36e-03 | 2.83e-02 | 19 |
| GO:00434878 | Breast | Precancer | regulation of RNA stability | 19/1080 | 170/18723 | 4.38e-03 | 3.42e-02 | 19 |
| 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:000641714 | Breast | IDC | regulation of translation | 74/1434 | 468/18723 | 1.67e-09 | 1.53e-07 | 74 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 |
| 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 |
| Page: 1 2 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| Page: 1 2 |
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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 |
| Page: 1 |
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