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Gene: SELENOS |
Gene summary for SELENOS |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SELENOS | Gene ID | 55829 |
| Gene name | selenoprotein S | |
| Gene Alias | AD-015 | |
| Cytomap | 15q26.3 | |
| Gene Type | protein-coding | GO ID | GO:0000271 | UniProtAcc | Q9BQE4 |
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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 |
| 55829 | SELENOS | GSM4909281 | Human | Breast | IDC | 6.44e-11 | 4.14e-01 | 0.21 |
| 55829 | SELENOS | GSM4909282 | Human | Breast | IDC | 5.25e-32 | 8.01e-01 | -0.0288 |
| 55829 | SELENOS | GSM4909285 | Human | Breast | IDC | 2.52e-03 | 1.53e-01 | 0.21 |
| 55829 | SELENOS | GSM4909286 | Human | Breast | IDC | 2.99e-05 | 1.17e-01 | 0.1081 |
| 55829 | SELENOS | GSM4909287 | Human | Breast | IDC | 1.89e-05 | 3.69e-01 | 0.2057 |
| 55829 | SELENOS | GSM4909290 | Human | Breast | IDC | 2.12e-14 | 5.36e-01 | 0.2096 |
| 55829 | SELENOS | GSM4909291 | Human | Breast | IDC | 9.81e-27 | 7.99e-01 | 0.1753 |
| 55829 | SELENOS | GSM4909292 | Human | Breast | IDC | 1.19e-07 | 7.74e-01 | 0.1236 |
| 55829 | SELENOS | GSM4909293 | Human | Breast | IDC | 1.30e-04 | 9.84e-02 | 0.1581 |
| 55829 | SELENOS | GSM4909295 | Human | Breast | IDC | 1.25e-10 | 5.84e-01 | 0.0898 |
| 55829 | SELENOS | GSM4909298 | Human | Breast | IDC | 7.72e-05 | 1.92e-01 | 0.1551 |
| 55829 | SELENOS | GSM4909304 | Human | Breast | IDC | 7.69e-05 | 2.79e-01 | 0.1636 |
| 55829 | SELENOS | GSM4909305 | Human | Breast | IDC | 2.68e-05 | 3.56e-01 | 0.0436 |
| 55829 | SELENOS | GSM4909307 | Human | Breast | IDC | 4.97e-03 | 3.55e-01 | 0.1569 |
| 55829 | SELENOS | GSM4909308 | Human | Breast | IDC | 1.38e-11 | 4.08e-01 | 0.158 |
| 55829 | SELENOS | GSM4909309 | Human | Breast | IDC | 9.07e-03 | 3.01e-01 | 0.0483 |
| 55829 | SELENOS | GSM4909311 | Human | Breast | IDC | 7.48e-16 | 1.54e-01 | 0.1534 |
| 55829 | SELENOS | GSM4909312 | Human | Breast | IDC | 1.47e-08 | 4.59e-01 | 0.1552 |
| 55829 | SELENOS | GSM4909317 | Human | Breast | IDC | 2.23e-08 | 3.54e-01 | 0.1355 |
| 55829 | SELENOS | GSM4909319 | Human | Breast | IDC | 3.32e-19 | 1.12e-01 | 0.1563 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:190357320 | Esophagus | HGIN | negative regulation of response to endoplasmic reticulum stress | 18/2587 | 44/18723 | 8.97e-06 | 2.64e-04 | 18 |
| GO:190223620 | Esophagus | HGIN | negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway | 11/2587 | 20/18723 | 1.73e-05 | 4.71e-04 | 11 |
| GO:003096817 | Esophagus | HGIN | endoplasmic reticulum unfolded protein response | 24/2587 | 74/18723 | 3.39e-05 | 8.61e-04 | 24 |
| GO:003459926 | Esophagus | HGIN | cellular response to oxidative stress | 65/2587 | 288/18723 | 3.42e-05 | 8.66e-04 | 65 |
| GO:004346718 | Esophagus | HGIN | regulation of generation of precursor metabolites and energy | 34/2587 | 130/18723 | 1.37e-04 | 2.76e-03 | 34 |
| GO:00309706 | Esophagus | HGIN | retrograde protein transport, ER to cytosol | 12/2587 | 29/18723 | 2.48e-04 | 4.38e-03 | 12 |
| GO:19035136 | Esophagus | HGIN | endoplasmic reticulum to cytosol transport | 12/2587 | 29/18723 | 2.48e-04 | 4.38e-03 | 12 |
| GO:199074820 | Esophagus | HGIN | cellular detoxification | 30/2587 | 116/18723 | 4.05e-04 | 6.15e-03 | 30 |
| GO:00365036 | Esophagus | HGIN | ERAD pathway | 27/2587 | 107/18723 | 1.15e-03 | 1.39e-02 | 27 |
| GO:009723720 | Esophagus | HGIN | cellular response to toxic substance | 30/2587 | 124/18723 | 1.32e-03 | 1.57e-02 | 30 |
| GO:00325277 | Esophagus | HGIN | protein exit from endoplasmic reticulum | 15/2587 | 48/18723 | 1.49e-03 | 1.73e-02 | 15 |
| GO:004343420 | Esophagus | HGIN | response to peptide hormone | 79/2587 | 414/18723 | 1.60e-03 | 1.79e-02 | 79 |
| GO:00304335 | Esophagus | HGIN | ubiquitin-dependent ERAD pathway | 22/2587 | 85/18723 | 2.24e-03 | 2.31e-02 | 22 |
| GO:009886920 | Esophagus | HGIN | cellular oxidant detoxification | 25/2587 | 101/18723 | 2.29e-03 | 2.34e-02 | 25 |
| GO:190165318 | Esophagus | HGIN | cellular response to peptide | 68/2587 | 359/18723 | 3.88e-03 | 3.54e-02 | 68 |
| GO:000974326 | Esophagus | HGIN | response to carbohydrate | 50/2587 | 253/18723 | 5.27e-03 | 4.35e-02 | 50 |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:0043161111 | Esophagus | ESCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 312/8552 | 412/18723 | 3.53e-36 | 4.48e-33 | 312 |
| GO:0097193111 | Esophagus | ESCC | intrinsic apoptotic signaling pathway | 222/8552 | 288/18723 | 5.87e-28 | 2.02e-25 | 222 |
| GO:2001233111 | Esophagus | ESCC | regulation of apoptotic signaling pathway | 256/8552 | 356/18723 | 4.11e-24 | 1.04e-21 | 256 |
| 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 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414118 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
| hsa0414119 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
| hsa0414124 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
| hsa0414134 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
| hsa0414143 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
| hsa0414153 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
| hsa0414120 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
| hsa04141110 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
| hsa04141 | Colorectum | AD | Protein processing in endoplasmic reticulum | 80/2092 | 174/8465 | 5.96e-10 | 1.25e-08 | 7.96e-09 | 80 |
| hsa041411 | Colorectum | AD | Protein processing in endoplasmic reticulum | 80/2092 | 174/8465 | 5.96e-10 | 1.25e-08 | 7.96e-09 | 80 |
| hsa041412 | Colorectum | SER | Protein processing in endoplasmic reticulum | 60/1580 | 174/8465 | 4.20e-07 | 7.33e-06 | 5.32e-06 | 60 |
| hsa041413 | Colorectum | SER | Protein processing in endoplasmic reticulum | 60/1580 | 174/8465 | 4.20e-07 | 7.33e-06 | 5.32e-06 | 60 |
| hsa041414 | Colorectum | MSS | Protein processing in endoplasmic reticulum | 75/1875 | 174/8465 | 3.78e-10 | 8.44e-09 | 5.17e-09 | 75 |
| hsa041415 | Colorectum | MSS | Protein processing in endoplasmic reticulum | 75/1875 | 174/8465 | 3.78e-10 | 8.44e-09 | 5.17e-09 | 75 |
| hsa041418 | Colorectum | FAP | Protein processing in endoplasmic reticulum | 50/1404 | 174/8465 | 3.64e-05 | 3.68e-04 | 2.24e-04 | 50 |
| hsa041419 | Colorectum | FAP | Protein processing in endoplasmic reticulum | 50/1404 | 174/8465 | 3.64e-05 | 3.68e-04 | 2.24e-04 | 50 |
| hsa0414126 | Endometrium | AEH | Protein processing in endoplasmic reticulum | 62/1197 | 174/8465 | 5.97e-13 | 1.39e-11 | 1.01e-11 | 62 |
| hsa04141111 | Endometrium | AEH | Protein processing in endoplasmic reticulum | 62/1197 | 174/8465 | 5.97e-13 | 1.39e-11 | 1.01e-11 | 62 |
| hsa0414127 | Endometrium | EEC | Protein processing in endoplasmic reticulum | 64/1237 | 174/8465 | 2.17e-13 | 5.09e-12 | 3.80e-12 | 64 |
| hsa0414136 | Endometrium | EEC | Protein processing in endoplasmic reticulum | 64/1237 | 174/8465 | 2.17e-13 | 5.09e-12 | 3.80e-12 | 64 |
| 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 |
| SELENOS | SNV | Missense_Mutation | rs751562043 | c.539N>A | p.Arg180His | p.R180H | Q9BQE4 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-BH-A1FC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SELENOS | SNV | Missense_Mutation | c.455N>T | p.Lys152Ile | p.K152I | Q9BQE4 | protein_coding | deleterious(0) | possibly_damaging(0.803) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| SELENOS | SNV | Missense_Mutation | novel | c.101G>A | p.Gly34Asp | p.G34D | Q9BQE4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A7WJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SELENOS | SNV | Missense_Mutation | c.331N>C | p.Lys111Gln | p.K111Q | Q9BQE4 | protein_coding | deleterious(0.01) | possibly_damaging(0.602) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SELENOS | SNV | Missense_Mutation | novel | c.221N>C | p.Val74Ala | p.V74A | Q9BQE4 | protein_coding | tolerated(0.54) | benign(0.038) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SELENOS | SNV | Missense_Mutation | novel | c.361N>C | p.Ser121Arg | p.S121R | Q9BQE4 | protein_coding | tolerated(0.17) | benign(0.067) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| SELENOS | SNV | Missense_Mutation | c.328N>C | p.Glu110Gln | p.E110Q | Q9BQE4 | protein_coding | tolerated(0.24) | benign(0.006) | TCGA-55-A48Y-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | CR | |
| SELENOS | SNV | Missense_Mutation | novel | c.292N>C | p.Glu98Gln | p.E98Q | Q9BQE4 | protein_coding | deleterious(0.02) | possibly_damaging(0.686) | TCGA-22-1016-01 | Lung | lung squamous cell carcinoma | Male | >=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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