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Gene: LSM14A |
Gene summary for LSM14A |
Gene summary. |
Gene information | Species | Human | Gene symbol | LSM14A | Gene ID | 26065 |
Gene name | LSM14A mRNA processing body assembly factor | |
Gene Alias | C19orf13 | |
Cytomap | 19q13.11 | |
Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | Q8ND56 |
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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 |
26065 | LSM14A | CA_HPV_3 | Human | Cervix | CC | 1.29e-02 | 1.01e-01 | 0.0414 |
26065 | LSM14A | CCI_1 | Human | Cervix | CC | 1.72e-02 | 4.84e-01 | 0.528 |
26065 | LSM14A | CCI_2 | Human | Cervix | CC | 2.28e-06 | 7.43e-01 | 0.5249 |
26065 | LSM14A | CCI_3 | Human | Cervix | CC | 2.90e-04 | 6.28e-01 | 0.516 |
26065 | LSM14A | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.75e-09 | -4.16e-01 | 0.0155 |
26065 | LSM14A | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.83e-02 | 4.43e-01 | 0.281 |
26065 | LSM14A | A001-C-207 | Human | Colorectum | FAP | 1.10e-03 | -2.48e-01 | 0.1278 |
26065 | LSM14A | A015-C-203 | Human | Colorectum | FAP | 1.51e-26 | -4.68e-01 | -0.1294 |
26065 | LSM14A | A015-C-204 | Human | Colorectum | FAP | 3.00e-08 | -2.24e-01 | -0.0228 |
26065 | LSM14A | A014-C-040 | Human | Colorectum | FAP | 8.16e-07 | -5.55e-01 | -0.1184 |
26065 | LSM14A | A002-C-201 | Human | Colorectum | FAP | 4.07e-16 | -3.64e-01 | 0.0324 |
26065 | LSM14A | A002-C-203 | Human | Colorectum | FAP | 1.04e-05 | -1.76e-01 | 0.2786 |
26065 | LSM14A | A001-C-119 | Human | Colorectum | FAP | 2.04e-08 | -3.36e-01 | -0.1557 |
26065 | LSM14A | A001-C-108 | Human | Colorectum | FAP | 4.55e-19 | -3.33e-01 | -0.0272 |
26065 | LSM14A | A002-C-205 | Human | Colorectum | FAP | 2.57e-26 | -4.64e-01 | -0.1236 |
26065 | LSM14A | A014-C-108 | Human | Colorectum | FAP | 2.75e-03 | -4.01e-01 | -0.124 |
26065 | LSM14A | A001-C-104 | Human | Colorectum | FAP | 2.27e-09 | -3.63e-01 | 0.0184 |
26065 | LSM14A | A015-C-005 | Human | Colorectum | FAP | 2.26e-07 | -3.65e-01 | -0.0336 |
26065 | LSM14A | A015-C-006 | Human | Colorectum | FAP | 4.76e-18 | -4.91e-01 | -0.0994 |
26065 | LSM14A | A015-C-106 | Human | Colorectum | FAP | 3.04e-11 | -2.80e-01 | -0.0511 |
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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:00321035 | Cervix | CC | positive regulation of response to external stimulus | 95/2311 | 427/18723 | 5.44e-09 | 5.03e-07 | 95 |
GO:00027644 | Cervix | CC | immune response-regulating signaling pathway | 97/2311 | 468/18723 | 1.49e-07 | 7.07e-06 | 97 |
GO:00305229 | Cervix | CC | intracellular receptor signaling pathway | 60/2311 | 265/18723 | 1.89e-06 | 5.97e-05 | 60 |
GO:00313494 | Cervix | CC | positive regulation of defense response | 60/2311 | 278/18723 | 9.38e-06 | 2.11e-04 | 60 |
GO:00028315 | Cervix | CC | regulation of response to biotic stimulus | 67/2311 | 327/18723 | 1.79e-05 | 3.36e-04 | 67 |
GO:000641710 | Cervix | CC | regulation of translation | 89/2311 | 468/18723 | 1.86e-05 | 3.46e-04 | 89 |
GO:00096158 | Cervix | CC | response to virus | 73/2311 | 367/18723 | 2.22e-05 | 3.95e-04 | 73 |
GO:00022212 | Cervix | CC | pattern recognition receptor signaling pathway | 39/2311 | 172/18723 | 1.08e-04 | 1.38e-03 | 39 |
GO:00027534 | Cervix | CC | cytoplasmic pattern recognition receptor signaling pathway | 18/2311 | 60/18723 | 2.26e-04 | 2.55e-03 | 18 |
GO:00192213 | Cervix | CC | cytokine-mediated signaling pathway | 84/2311 | 472/18723 | 3.25e-04 | 3.44e-03 | 84 |
GO:00450882 | Cervix | CC | regulation of innate immune response | 44/2311 | 218/18723 | 6.40e-04 | 5.97e-03 | 44 |
GO:00395292 | Cervix | CC | RIG-I signaling pathway | 10/2311 | 27/18723 | 9.25e-04 | 7.84e-03 | 10 |
GO:00028331 | Cervix | CC | positive regulation of response to biotic stimulus | 35/2311 | 168/18723 | 1.23e-03 | 9.87e-03 | 35 |
GO:00985863 | Cervix | CC | cellular response to virus | 20/2311 | 84/18723 | 2.62e-03 | 1.81e-02 | 20 |
GO:00395281 | Cervix | CC | cytoplasmic pattern recognition receptor signaling pathway in response to virus | 10/2311 | 34/18723 | 6.40e-03 | 3.58e-02 | 10 |
GO:00019612 | Cervix | CC | positive regulation of cytokine-mediated signaling pathway | 13/2311 | 50/18723 | 6.42e-03 | 3.58e-02 | 13 |
GO:01400143 | Cervix | CC | mitotic nuclear division | 50/2311 | 287/18723 | 7.27e-03 | 3.91e-02 | 50 |
GO:00607602 | Cervix | CC | positive regulation of response to cytokine stimulus | 14/2311 | 57/18723 | 8.17e-03 | 4.25e-02 | 14 |
GO:0045089 | Cervix | CC | positive regulation of innate immune response | 26/2311 | 131/18723 | 9.33e-03 | 4.66e-02 | 26 |
GO:00482851 | Cervix | CC | organelle fission | 78/2311 | 488/18723 | 9.70e-03 | 4.79e-02 | 78 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
LSM14A | insertion | Frame_Shift_Ins | novel | c.1088_1089insT | p.Asp364Ter | p.D364* | Q8ND56 | protein_coding | TCGA-F7-A623-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
LSM14A | insertion | Frame_Shift_Ins | novel | c.253dupT | p.Cys85LeufsTer76 | p.C85Lfs*76 | Q8ND56 | protein_coding | TCGA-VP-A87H-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | SD | ||
LSM14A | SNV | Missense_Mutation | c.352N>T | p.Pro118Ser | p.P118S | Q8ND56 | protein_coding | tolerated(0.1) | benign(0.199) | TCGA-BR-4257-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
LSM14A | SNV | Missense_Mutation | c.1243N>A | p.Leu415Ile | p.L415I | Q8ND56 | protein_coding | tolerated_low_confidence(0.44) | benign(0.001) | TCGA-BR-6852-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LSM14A | SNV | Missense_Mutation | c.548N>C | p.Ser183Thr | p.S183T | Q8ND56 | protein_coding | tolerated(0.15) | benign(0.041) | TCGA-EQ-8122-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
LSM14A | SNV | Missense_Mutation | c.1288N>G | p.Thr430Ala | p.T430A | Q8ND56 | protein_coding | tolerated(0.23) | benign(0) | TCGA-HU-A4GT-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | copolang | SD | |
LSM14A | SNV | Missense_Mutation | c.815G>A | p.Arg272His | p.R272H | Q8ND56 | protein_coding | deleterious(0.01) | probably_damaging(0.93) | TCGA-RD-A8NB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
LSM14A | SNV | Missense_Mutation | novel | c.40N>A | p.Leu14Ile | p.L14I | Q8ND56 | protein_coding | deleterious(0) | possibly_damaging(0.656) | TCGA-VQ-A91E-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | CR |
LSM14A | deletion | Frame_Shift_Del | novel | c.827delN | p.Gly277ValfsTer14 | p.G277Vfs*14 | Q8ND56 | protein_coding | TCGA-HF-7132-01 | Stomach | stomach adenocarcinoma | Male | Unknown | I/II | Chemotherapy | fluorouracil | 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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