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Gene: SELENOF |
Gene summary for SELENOF |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SELENOF | Gene ID | 9403 |
| Gene name | selenoprotein F | |
| Gene Alias | SEP15 | |
| Cytomap | 1p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0006457 | UniProtAcc | O60613 |
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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 |
| 9403 | SELENOF | HTA11_347_2000001011 | Human | Colorectum | AD | 5.55e-09 | 5.27e-01 | -0.1954 |
| 9403 | SELENOF | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.84e-22 | -4.37e-01 | 0.294 |
| 9403 | SELENOF | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.06e-07 | -4.37e-01 | 0.281 |
| 9403 | SELENOF | HTA11_99999971662_82457 | Human | Colorectum | MSS | 6.91e-23 | -4.37e-01 | 0.3859 |
| 9403 | SELENOF | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.50e-05 | -4.37e-01 | 0.2585 |
| 9403 | SELENOF | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.11e-21 | -4.37e-01 | 0.3005 |
| 9403 | SELENOF | A015-C-203 | Human | Colorectum | FAP | 2.50e-16 | -3.22e-01 | -0.1294 |
| 9403 | SELENOF | A015-C-204 | Human | Colorectum | FAP | 4.42e-03 | -2.47e-01 | -0.0228 |
| 9403 | SELENOF | A014-C-040 | Human | Colorectum | FAP | 3.40e-02 | -3.88e-01 | -0.1184 |
| 9403 | SELENOF | A002-C-201 | Human | Colorectum | FAP | 5.99e-08 | -2.79e-01 | 0.0324 |
| 9403 | SELENOF | A002-C-203 | Human | Colorectum | FAP | 1.12e-02 | -1.28e-01 | 0.2786 |
| 9403 | SELENOF | A001-C-119 | Human | Colorectum | FAP | 2.91e-04 | -2.22e-01 | -0.1557 |
| 9403 | SELENOF | A001-C-108 | Human | Colorectum | FAP | 1.70e-07 | -2.69e-01 | -0.0272 |
| 9403 | SELENOF | A002-C-205 | Human | Colorectum | FAP | 1.85e-12 | -3.41e-01 | -0.1236 |
| 9403 | SELENOF | A015-C-005 | Human | Colorectum | FAP | 1.72e-03 | -2.57e-01 | -0.0336 |
| 9403 | SELENOF | A015-C-006 | Human | Colorectum | FAP | 1.12e-09 | -3.93e-01 | -0.0994 |
| 9403 | SELENOF | A015-C-106 | Human | Colorectum | FAP | 8.27e-09 | -2.26e-01 | -0.0511 |
| 9403 | SELENOF | A002-C-114 | Human | Colorectum | FAP | 3.43e-11 | -3.67e-01 | -0.1561 |
| 9403 | SELENOF | A015-C-104 | Human | Colorectum | FAP | 9.78e-17 | -3.52e-01 | -0.1899 |
| 9403 | SELENOF | A001-C-014 | Human | Colorectum | FAP | 6.95e-08 | -2.73e-01 | 0.0135 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| 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 | ||
| 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:000645812 | Liver | HCC | 'de novo' protein folding | 36/7958 | 43/18723 | 3.15e-08 | 7.10e-07 | 36 |
| GO:005108412 | Liver | HCC | 'de novo' posttranslational protein folding | 32/7958 | 39/18723 | 4.73e-07 | 7.69e-06 | 32 |
| GO:000645716 | Prostate | BPH | protein folding | 85/3107 | 212/18723 | 2.37e-16 | 4.74e-14 | 85 |
| GO:000645816 | Prostate | BPH | 'de novo' protein folding | 23/3107 | 43/18723 | 3.33e-08 | 9.46e-07 | 23 |
| GO:005108416 | Prostate | BPH | 'de novo' posttranslational protein folding | 20/3107 | 39/18723 | 6.46e-07 | 1.26e-05 | 20 |
| GO:000645717 | Prostate | Tumor | protein folding | 85/3246 | 212/18723 | 3.37e-15 | 5.37e-13 | 85 |
| GO:000645817 | Prostate | Tumor | 'de novo' protein folding | 23/3246 | 43/18723 | 7.73e-08 | 2.14e-06 | 23 |
| GO:005108417 | Prostate | Tumor | 'de novo' posttranslational protein folding | 20/3246 | 39/18723 | 1.33e-06 | 2.42e-05 | 20 |
| GO:00064576 | Stomach | GC | protein folding | 42/1159 | 212/18723 | 1.46e-11 | 3.31e-09 | 42 |
| GO:00064586 | Stomach | GC | 'de novo' protein folding | 15/1159 | 43/18723 | 2.01e-08 | 1.63e-06 | 15 |
| GO:00510846 | Stomach | GC | 'de novo' posttranslational protein folding | 13/1159 | 39/18723 | 3.28e-07 | 1.75e-05 | 13 |
| GO:000645711 | Stomach | CAG with IM | protein folding | 42/1050 | 212/18723 | 5.92e-13 | 2.11e-10 | 42 |
| GO:000645811 | Stomach | CAG with IM | 'de novo' protein folding | 15/1050 | 43/18723 | 5.31e-09 | 5.25e-07 | 15 |
| GO:005108411 | Stomach | CAG with IM | 'de novo' posttranslational protein folding | 13/1050 | 39/18723 | 1.04e-07 | 7.14e-06 | 13 |
| GO:000645721 | Stomach | CSG | protein folding | 42/1034 | 212/18723 | 3.56e-13 | 1.26e-10 | 42 |
| GO:000645821 | Stomach | CSG | 'de novo' protein folding | 15/1034 | 43/18723 | 4.31e-09 | 4.57e-07 | 15 |
| GO:005108421 | Stomach | CSG | 'de novo' posttranslational protein folding | 13/1034 | 39/18723 | 8.73e-08 | 6.33e-06 | 13 |
| GO:0006457112 | Thyroid | PTC | protein folding | 137/5968 | 212/18723 | 8.29e-23 | 2.01e-20 | 137 |
| GO:0006458112 | Thyroid | PTC | 'de novo' protein folding | 28/5968 | 43/18723 | 7.63e-06 | 8.82e-05 | 28 |
| GO:0051084112 | Thyroid | PTC | 'de novo' posttranslational protein folding | 25/5968 | 39/18723 | 3.50e-05 | 3.30e-04 | 25 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| SELENOF | SNV | Missense_Mutation | rs375315291 | c.23N>T | p.Pro8Leu | p.P8L | protein_coding | tolerated_low_confidence(0.24) | benign(0) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| SELENOF | SNV | Missense_Mutation | novel | c.92N>T | p.Ala31Val | p.A31V | protein_coding | tolerated(0.42) | benign(0.001) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SELENOF | SNV | Missense_Mutation | novel | c.337N>T | p.Pro113Ser | p.P113S | protein_coding | deleterious(0.01) | possibly_damaging(0.617) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SELENOF | SNV | Missense_Mutation | c.463G>C | p.Glu155Gln | p.E155Q | protein_coding | tolerated(0.11) | probably_damaging(0.987) | TCGA-95-7944-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| SELENOF | SNV | Missense_Mutation | novel | c.40C>T | p.Pro14Ser | p.P14S | protein_coding | deleterious_low_confidence(0) | benign(0.006) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD | |
| SELENOF | SNV | Missense_Mutation | novel | c.449N>G | p.Asn150Ser | p.N150S | protein_coding | deleterious(0.01) | probably_damaging(0.995) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | ||
| SELENOF | SNV | Missense_Mutation | novel | c.443N>G | p.Lys148Arg | p.K148R | protein_coding | tolerated(0.07) | probably_damaging(0.996) | TCGA-VQ-A8PO-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 |
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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 |
| Page: 1 |
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