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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:200124233 | Thyroid | ATC | regulation of intrinsic apoptotic signaling pathway | 103/6293 | 164/18723 | 1.67e-14 | 9.77e-13 | 103 |
| GO:003459934 | Thyroid | ATC | cellular response to oxidative stress | 158/6293 | 288/18723 | 7.35e-14 | 3.94e-12 | 158 |
| GO:2001234210 | Thyroid | ATC | negative regulation of apoptotic signaling pathway | 129/6293 | 224/18723 | 1.26e-13 | 6.46e-12 | 129 |
| GO:000698633 | Thyroid | ATC | response to unfolded protein | 88/6293 | 137/18723 | 2.04e-13 | 9.91e-12 | 88 |
| GO:003650322 | Thyroid | ATC | ERAD pathway | 72/6293 | 107/18723 | 1.05e-12 | 4.41e-11 | 72 |
| GO:003043322 | Thyroid | ATC | ubiquitin-dependent ERAD pathway | 60/6293 | 85/18723 | 3.38e-12 | 1.38e-10 | 60 |
| GO:003596733 | Thyroid | ATC | cellular response to topologically incorrect protein | 74/6293 | 116/18723 | 2.69e-11 | 9.20e-10 | 74 |
| GO:200124333 | Thyroid | ATC | negative regulation of intrinsic apoptotic signaling pathway | 63/6293 | 98/18723 | 4.97e-10 | 1.33e-08 | 63 |
| GO:003462033 | Thyroid | ATC | cellular response to unfolded protein | 61/6293 | 96/18723 | 1.84e-09 | 4.52e-08 | 61 |
| GO:190589728 | Thyroid | ATC | regulation of response to endoplasmic reticulum stress | 54/6293 | 82/18723 | 2.34e-09 | 5.58e-08 | 54 |
| GO:190165325 | Thyroid | ATC | cellular response to peptide | 173/6293 | 359/18723 | 5.87e-09 | 1.28e-07 | 173 |
| GO:003096823 | Thyroid | ATC | endoplasmic reticulum unfolded protein response | 49/6293 | 74/18723 | 9.75e-09 | 2.03e-07 | 49 |
| GO:0070059113 | Thyroid | ATC | intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress | 43/6293 | 63/18723 | 1.98e-08 | 3.90e-07 | 43 |
| GO:004343428 | Thyroid | ATC | response to peptide hormone | 192/6293 | 414/18723 | 3.63e-08 | 6.70e-07 | 192 |
| GO:190357327 | Thyroid | ATC | negative regulation of response to endoplasmic reticulum stress | 32/6293 | 44/18723 | 1.28e-07 | 2.12e-06 | 32 |
| GO:007137524 | Thyroid | ATC | cellular response to peptide hormone stimulus | 138/6293 | 290/18723 | 4.90e-07 | 7.05e-06 | 138 |
| GO:003097015 | Thyroid | ATC | retrograde protein transport, ER to cytosol | 23/6293 | 29/18723 | 5.84e-07 | 8.19e-06 | 23 |
| GO:190351315 | Thyroid | ATC | endoplasmic reticulum to cytosol transport | 23/6293 | 29/18723 | 5.84e-07 | 8.19e-06 | 23 |
| GO:000698424 | Thyroid | ATC | ER-nucleus signaling pathway | 32/6293 | 46/18723 | 6.68e-07 | 9.13e-06 | 32 |
| GO:003286824 | Thyroid | ATC | response to insulin | 126/6293 | 264/18723 | 1.24e-06 | 1.59e-05 | 126 |
| 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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