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Gene: PLS1 |
Gene summary for PLS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PLS1 | Gene ID | 5357 |
| Gene name | plastin 1 | |
| Gene Alias | DFNA76 | |
| Cytomap | 3q23 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q14651 |
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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 |
| 5357 | PLS1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.57e-19 | -6.11e-01 | 0.0155 |
| 5357 | PLS1 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.66e-08 | 5.69e-01 | -0.1954 |
| 5357 | PLS1 | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.69e-03 | -4.50e-01 | -0.0179 |
| 5357 | PLS1 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.49e-16 | -5.58e-01 | 0.096 |
| 5357 | PLS1 | HTA11_9408_2000001011 | Human | Colorectum | AD | 1.34e-02 | -7.58e-01 | 0.0451 |
| 5357 | PLS1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 5.73e-03 | -5.71e-01 | 0.0528 |
| 5357 | PLS1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 5.76e-03 | -4.62e-01 | 0.0338 |
| 5357 | PLS1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.68e-10 | -4.40e-01 | 0.0674 |
| 5357 | PLS1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.77e-04 | -3.89e-01 | 0.0588 |
| 5357 | PLS1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.82e-13 | -4.81e-01 | 0.294 |
| 5357 | PLS1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.32e-02 | -3.58e-01 | 0.3859 |
| 5357 | PLS1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.87e-09 | -7.65e-01 | 0.2585 |
| 5357 | PLS1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 6.15e-24 | -6.49e-01 | 0.3005 |
| 5357 | PLS1 | F007 | Human | Colorectum | FAP | 1.77e-08 | -4.65e-01 | 0.1176 |
| 5357 | PLS1 | A002-C-010 | Human | Colorectum | FAP | 4.19e-06 | -1.89e-01 | 0.242 |
| 5357 | PLS1 | A001-C-207 | Human | Colorectum | FAP | 4.68e-05 | -2.93e-01 | 0.1278 |
| 5357 | PLS1 | A015-C-203 | Human | Colorectum | FAP | 4.80e-41 | -6.00e-01 | -0.1294 |
| 5357 | PLS1 | A015-C-204 | Human | Colorectum | FAP | 3.21e-11 | -4.73e-01 | -0.0228 |
| 5357 | PLS1 | A014-C-040 | Human | Colorectum | FAP | 1.72e-06 | -4.69e-01 | -0.1184 |
| 5357 | PLS1 | A002-C-201 | Human | Colorectum | FAP | 1.90e-19 | -4.97e-01 | 0.0324 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:0040014 | Colorectum | FAP | regulation of multicellular organism growth | 16/2622 | 61/18723 | 8.38e-03 | 4.89e-02 | 16 |
| GO:00226002 | Colorectum | FAP | digestive system process | 24/2622 | 104/18723 | 8.41e-03 | 4.89e-02 | 24 |
| GO:00508922 | Colorectum | FAP | intestinal absorption | 12/2622 | 41/18723 | 8.57e-03 | 4.96e-02 | 12 |
| GO:00726595 | Colorectum | CRC | protein localization to plasma membrane | 80/2078 | 284/18723 | 1.36e-15 | 4.07e-12 | 80 |
| GO:00070155 | Colorectum | CRC | actin filament organization | 104/2078 | 442/18723 | 4.75e-14 | 7.12e-11 | 104 |
| GO:19907785 | Colorectum | CRC | protein localization to cell periphery | 85/2078 | 333/18723 | 8.75e-14 | 1.05e-10 | 85 |
| GO:00020645 | Colorectum | CRC | epithelial cell development | 55/2078 | 220/18723 | 4.63e-09 | 1.16e-06 | 55 |
| GO:00325354 | Colorectum | CRC | regulation of cellular component size | 79/2078 | 383/18723 | 3.30e-08 | 4.60e-06 | 79 |
| GO:19043754 | Colorectum | CRC | regulation of protein localization to cell periphery | 36/2078 | 125/18723 | 4.62e-08 | 5.91e-06 | 36 |
| GO:19054754 | Colorectum | CRC | regulation of protein localization to membrane | 45/2078 | 175/18723 | 4.64e-08 | 5.91e-06 | 45 |
| GO:19038295 | Colorectum | CRC | positive regulation of cellular protein localization | 61/2078 | 276/18723 | 9.59e-08 | 1.17e-05 | 61 |
| GO:19030764 | Colorectum | CRC | regulation of protein localization to plasma membrane | 31/2078 | 104/18723 | 1.66e-07 | 1.72e-05 | 31 |
| GO:01060274 | Colorectum | CRC | neuron projection organization | 28/2078 | 93/18723 | 5.17e-07 | 3.73e-05 | 28 |
| GO:00615724 | Colorectum | CRC | actin filament bundle organization | 40/2078 | 161/18723 | 6.72e-07 | 4.52e-05 | 40 |
| GO:00510174 | Colorectum | CRC | actin filament bundle assembly | 39/2078 | 157/18723 | 9.26e-07 | 5.83e-05 | 39 |
| GO:00486383 | Colorectum | CRC | regulation of developmental growth | 64/2078 | 330/18723 | 5.74e-06 | 2.26e-04 | 64 |
| GO:19054774 | Colorectum | CRC | positive regulation of protein localization to membrane | 28/2078 | 106/18723 | 8.84e-06 | 3.11e-04 | 28 |
| GO:00459274 | Colorectum | CRC | positive regulation of growth | 51/2078 | 259/18723 | 3.23e-05 | 8.27e-04 | 51 |
| GO:19043774 | Colorectum | CRC | positive regulation of protein localization to cell periphery | 20/2078 | 69/18723 | 3.92e-05 | 9.54e-04 | 20 |
| GO:00308664 | Colorectum | CRC | cortical actin cytoskeleton organization | 14/2078 | 40/18723 | 5.81e-05 | 1.31e-03 | 14 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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. |
| 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 |
| PLS1 | SNV | Missense_Mutation | c.1849N>C | p.Phe617Leu | p.F617L | Q14651 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PLS1 | SNV | Missense_Mutation | c.1712N>A | p.Arg571Lys | p.R571K | Q14651 | protein_coding | tolerated(1) | benign(0) | TCGA-E9-A1RH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
| PLS1 | SNV | Missense_Mutation | rs773749532 | c.1526C>T | p.Ser509Leu | p.S509L | Q14651 | protein_coding | deleterious(0.02) | probably_damaging(0.988) | TCGA-EW-A1OV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | epirubicin | SD |
| PLS1 | SNV | Missense_Mutation | novel | c.605N>G | p.Ser202Cys | p.S202C | Q14651 | protein_coding | deleterious(0) | probably_damaging(0.965) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| PLS1 | insertion | Frame_Shift_Ins | novel | c.1245_1246insAAAAA | p.His416LysfsTer12 | p.H416Kfs*12 | Q14651 | protein_coding | TCGA-A8-A08C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PLS1 | insertion | In_Frame_Ins | novel | c.1246_1247insAAA | p.His416delinsGlnAsn | p.H416delinsQN | Q14651 | protein_coding | TCGA-A8-A08C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PLS1 | insertion | Nonsense_Mutation | novel | c.1534_1535insGAGAGGGGTAATGTTCATTTTATGATACAGATCTCTGGGCAGGGGTAAGAGA | p.Glu515Ter | p.E515* | Q14651 | protein_coding | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| PLS1 | SNV | Missense_Mutation | c.233N>T | p.Ser78Leu | p.S78L | Q14651 | protein_coding | tolerated(0.07) | benign(0.272) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| PLS1 | SNV | Missense_Mutation | c.1515N>C | p.Leu505Phe | p.L505F | Q14651 | protein_coding | deleterious(0.03) | possibly_damaging(0.521) | TCGA-EK-A3GJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PLS1 | SNV | Missense_Mutation | c.529N>C | p.Ile177Leu | p.I177L | Q14651 | protein_coding | deleterious(0) | benign(0.179) | TCGA-IR-A3LC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unspecific | Cisplatin | Complete Response |
| Page: 1 2 3 4 5 6 7 |
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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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