|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: SELENOK |
Gene summary for SELENOK |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SELENOK | Gene ID | 58515 |
| Gene name | selenoprotein K | |
| Gene Alias | HSPC030 | |
| Cytomap | 3p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | Q9Y6D0 |
Top |
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 |
| 58515 | SELENOK | GSM4909281 | Human | Breast | IDC | 5.58e-16 | 5.46e-01 | 0.21 |
| 58515 | SELENOK | GSM4909285 | Human | Breast | IDC | 4.55e-05 | 1.21e-01 | 0.21 |
| 58515 | SELENOK | GSM4909286 | Human | Breast | IDC | 1.45e-15 | 1.67e-01 | 0.1081 |
| 58515 | SELENOK | GSM4909290 | Human | Breast | IDC | 7.34e-11 | 3.76e-01 | 0.2096 |
| 58515 | SELENOK | GSM4909298 | Human | Breast | IDC | 1.90e-14 | 3.08e-01 | 0.1551 |
| 58515 | SELENOK | GSM4909299 | Human | Breast | IDC | 2.07e-04 | 3.12e-01 | 0.035 |
| 58515 | SELENOK | GSM4909300 | Human | Breast | IDC | 1.95e-02 | 3.29e-01 | 0.0334 |
| 58515 | SELENOK | GSM4909301 | Human | Breast | IDC | 5.13e-07 | 4.32e-01 | 0.1577 |
| 58515 | SELENOK | GSM4909305 | Human | Breast | IDC | 7.03e-07 | 2.18e-01 | 0.0436 |
| 58515 | SELENOK | GSM4909306 | Human | Breast | IDC | 3.92e-03 | 1.26e-01 | 0.1564 |
| 58515 | SELENOK | GSM4909308 | Human | Breast | IDC | 5.67e-15 | 2.86e-01 | 0.158 |
| 58515 | SELENOK | GSM4909311 | Human | Breast | IDC | 3.21e-13 | -1.64e-01 | 0.1534 |
| 58515 | SELENOK | GSM4909319 | Human | Breast | IDC | 8.35e-20 | -6.02e-02 | 0.1563 |
| 58515 | SELENOK | ctrl6 | Human | Breast | Precancer | 3.22e-20 | 7.21e-01 | -0.0061 |
| 58515 | SELENOK | brca1 | Human | Breast | Precancer | 1.06e-23 | -4.89e-01 | -0.0338 |
| 58515 | SELENOK | brca2 | Human | Breast | Precancer | 2.31e-20 | -4.89e-01 | -0.024 |
| 58515 | SELENOK | brca3 | Human | Breast | Precancer | 2.31e-20 | -4.89e-01 | -0.0263 |
| 58515 | SELENOK | brca10 | Human | Breast | Precancer | 2.97e-32 | 8.18e-01 | -0.0029 |
| 58515 | SELENOK | brca11 | Human | Breast | Precancer | 2.81e-02 | 6.74e-01 | 0.0193 |
| 58515 | SELENOK | M1 | Human | Breast | IDC | 1.90e-02 | 1.22e-01 | 0.1577 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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 |
| 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. |
Top |
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:00420987 | Breast | Precancer | T cell proliferation | 23/1080 | 199/18723 | 1.17e-03 | 1.27e-02 | 23 |
| GO:00421023 | Breast | Precancer | positive regulation of T cell proliferation | 14/1080 | 101/18723 | 1.94e-03 | 1.88e-02 | 14 |
| GO:00421296 | Breast | Precancer | regulation of T cell proliferation | 20/1080 | 171/18723 | 2.07e-03 | 1.97e-02 | 20 |
| GO:00506712 | Breast | Precancer | positive regulation of lymphocyte proliferation | 17/1080 | 137/18723 | 2.32e-03 | 2.16e-02 | 17 |
| GO:00324697 | Breast | Precancer | endoplasmic reticulum calcium ion homeostasis | 6/1080 | 25/18723 | 2.49e-03 | 2.28e-02 | 6 |
| GO:00329462 | Breast | Precancer | positive regulation of mononuclear cell proliferation | 17/1080 | 138/18723 | 2.51e-03 | 2.29e-02 | 17 |
| GO:00326406 | Breast | Precancer | tumor necrosis factor production | 20/1080 | 181/18723 | 4.01e-03 | 3.17e-02 | 20 |
| GO:00326806 | Breast | Precancer | regulation of tumor necrosis factor production | 20/1080 | 181/18723 | 4.01e-03 | 3.17e-02 | 20 |
| GO:00717066 | Breast | Precancer | tumor necrosis factor superfamily cytokine production | 20/1080 | 186/18723 | 5.43e-03 | 4.01e-02 | 20 |
| GO:19035556 | Breast | Precancer | regulation of tumor necrosis factor superfamily cytokine production | 20/1080 | 186/18723 | 5.43e-03 | 4.01e-02 | 20 |
| GO:00506704 | Breast | Precancer | regulation of lymphocyte proliferation | 23/1080 | 225/18723 | 5.62e-03 | 4.08e-02 | 23 |
| GO:0072503 | Breast | Precancer | cellular divalent inorganic cation homeostasis | 42/1080 | 486/18723 | 5.91e-03 | 4.21e-02 | 42 |
| GO:00706655 | Breast | Precancer | positive regulation of leukocyte proliferation | 17/1080 | 150/18723 | 5.92e-03 | 4.21e-02 | 17 |
| GO:00329443 | Breast | Precancer | regulation of mononuclear cell proliferation | 23/1080 | 227/18723 | 6.24e-03 | 4.40e-02 | 23 |
| GO:00327605 | Breast | Precancer | positive regulation of tumor necrosis factor production | 13/1080 | 103/18723 | 6.26e-03 | 4.40e-02 | 13 |
| GO:00716754 | Breast | Precancer | regulation of mononuclear cell migration | 14/1080 | 115/18723 | 6.42e-03 | 4.48e-02 | 14 |
| GO:009719314 | Breast | IDC | intrinsic apoptotic signaling pathway | 69/1434 | 288/18723 | 6.32e-18 | 2.99e-15 | 69 |
| GO:000697914 | Breast | IDC | response to oxidative stress | 83/1434 | 446/18723 | 2.36e-14 | 7.06e-12 | 83 |
| GO:003497614 | Breast | IDC | response to endoplasmic reticulum stress | 43/1434 | 256/18723 | 8.42e-07 | 3.82e-05 | 43 |
| GO:004578514 | Breast | IDC | positive regulation of cell adhesion | 62/1434 | 437/18723 | 1.70e-06 | 7.16e-05 | 62 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| SELENOK | SNV | Missense_Mutation | c.14N>G | p.Ser5Trp | p.S5W | protein_coding | deleterious(0) | possibly_damaging(0.829) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| SELENOK | SNV | Missense_Mutation | c.149N>A | p.Arg50Lys | p.R50K | protein_coding | tolerated(0.48) | benign(0.026) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SELENOK | SNV | Missense_Mutation | c.245N>A | p.Gly82Asp | p.G82D | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SELENOK | deletion | Frame_Shift_Del | novel | c.145delA | p.Arg49GlufsTer51 | p.R49Efs*51 | protein_coding | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |||
| SELENOK | SNV | Missense_Mutation | c.81N>A | p.Phe27Leu | p.F27L | protein_coding | deleterious(0.02) | probably_damaging(0.973) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| SELENOK | SNV | Missense_Mutation | rs376660375 | c.241N>T | p.Arg81Cys | p.R81C | protein_coding | deleterious(0.04) | benign(0.192) | TCGA-BG-A220-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SELENOK | deletion | Frame_Shift_Del | novel | c.145delN | p.Arg49GlufsTer51 | p.R49Efs*51 | protein_coding | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| Page: 1 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |