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Gene: SET |
Gene summary for SET |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SET | Gene ID | 6418 |
| Gene name | SET nuclear proto-oncogene | |
| Gene Alias | 2PP2A | |
| Cytomap | 9q34.11 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q01105 |
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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 |
| 6418 | SET | GSM4909281 | Human | Breast | IDC | 1.19e-12 | 4.38e-01 | 0.21 |
| 6418 | SET | GSM4909282 | Human | Breast | IDC | 5.84e-06 | 2.65e-01 | -0.0288 |
| 6418 | SET | GSM4909286 | Human | Breast | IDC | 1.21e-04 | 2.05e-01 | 0.1081 |
| 6418 | SET | GSM4909288 | Human | Breast | IDC | 4.01e-02 | 8.44e-02 | 0.0988 |
| 6418 | SET | GSM4909290 | Human | Breast | IDC | 1.06e-06 | 3.80e-01 | 0.2096 |
| 6418 | SET | GSM4909293 | Human | Breast | IDC | 3.04e-10 | 3.72e-01 | 0.1581 |
| 6418 | SET | GSM4909294 | Human | Breast | IDC | 1.30e-17 | 2.92e-01 | 0.2022 |
| 6418 | SET | GSM4909296 | Human | Breast | IDC | 3.02e-15 | -3.98e-01 | 0.1524 |
| 6418 | SET | GSM4909297 | Human | Breast | IDC | 1.76e-25 | 2.22e-01 | 0.1517 |
| 6418 | SET | GSM4909306 | Human | Breast | IDC | 7.23e-03 | -2.71e-01 | 0.1564 |
| 6418 | SET | GSM4909309 | Human | Breast | IDC | 2.00e-02 | -2.24e-01 | 0.0483 |
| 6418 | SET | GSM4909311 | Human | Breast | IDC | 3.37e-49 | -5.41e-01 | 0.1534 |
| 6418 | SET | GSM4909312 | Human | Breast | IDC | 1.00e-09 | -2.43e-01 | 0.1552 |
| 6418 | SET | GSM4909317 | Human | Breast | IDC | 1.36e-02 | 2.79e-01 | 0.1355 |
| 6418 | SET | GSM4909318 | Human | Breast | IDC | 4.71e-08 | 4.81e-01 | 0.2031 |
| 6418 | SET | GSM4909319 | Human | Breast | IDC | 1.16e-58 | -8.01e-01 | 0.1563 |
| 6418 | SET | GSM4909320 | Human | Breast | IDC | 5.01e-11 | -7.26e-01 | 0.1575 |
| 6418 | SET | GSM4909321 | Human | Breast | IDC | 1.85e-12 | -3.31e-01 | 0.1559 |
| 6418 | SET | brca10 | Human | Breast | Precancer | 1.12e-11 | -5.22e-01 | -0.0029 |
| 6418 | SET | M2 | Human | Breast | IDC | 7.97e-12 | 4.74e-01 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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 |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00709979 | Breast | Precancer | neuron death | 50/1080 | 361/18723 | 7.75e-09 | 5.70e-07 | 50 |
| GO:00514029 | Breast | Precancer | neuron apoptotic process | 38/1080 | 246/18723 | 2.68e-08 | 1.75e-06 | 38 |
| GO:19012149 | Breast | Precancer | regulation of neuron death | 41/1080 | 319/18723 | 1.27e-06 | 4.80e-05 | 41 |
| GO:00435237 | Breast | Precancer | regulation of neuron apoptotic process | 31/1080 | 212/18723 | 1.69e-06 | 6.08e-05 | 31 |
| GO:00224119 | Breast | Precancer | cellular component disassembly | 44/1080 | 443/18723 | 3.17e-04 | 4.51e-03 | 44 |
| GO:00435243 | Breast | Precancer | negative regulation of neuron apoptotic process | 19/1080 | 145/18723 | 6.83e-04 | 8.34e-03 | 19 |
| GO:00329865 | Breast | Precancer | protein-DNA complex disassembly | 6/1080 | 20/18723 | 6.99e-04 | 8.43e-03 | 6 |
| GO:19012157 | Breast | Precancer | negative regulation of neuron death | 24/1080 | 208/18723 | 9.50e-04 | 1.07e-02 | 24 |
| GO:007099714 | Breast | IDC | neuron death | 57/1434 | 361/18723 | 1.31e-07 | 7.38e-06 | 57 |
| GO:005140213 | Breast | IDC | neuron apoptotic process | 42/1434 | 246/18723 | 7.21e-07 | 3.35e-05 | 42 |
| GO:190121414 | Breast | IDC | regulation of neuron death | 48/1434 | 319/18723 | 5.01e-06 | 1.69e-04 | 48 |
| GO:004352313 | Breast | IDC | regulation of neuron apoptotic process | 35/1434 | 212/18723 | 1.26e-05 | 3.29e-04 | 35 |
| GO:000640113 | Breast | IDC | RNA catabolic process | 38/1434 | 278/18723 | 3.54e-04 | 5.16e-03 | 38 |
| GO:004352411 | Breast | IDC | negative regulation of neuron apoptotic process | 23/1434 | 145/18723 | 6.58e-04 | 8.11e-03 | 23 |
| GO:190121513 | Breast | IDC | negative regulation of neuron death | 29/1434 | 208/18723 | 1.23e-03 | 1.32e-02 | 29 |
| GO:190136112 | Breast | IDC | organic cyclic compound catabolic process | 56/1434 | 495/18723 | 2.12e-03 | 1.99e-02 | 56 |
| GO:004670012 | Breast | IDC | heterocycle catabolic process | 51/1434 | 445/18723 | 2.51e-03 | 2.25e-02 | 51 |
| GO:003298612 | Breast | IDC | protein-DNA complex disassembly | 6/1434 | 20/18723 | 3.03e-03 | 2.60e-02 | 6 |
| GO:003465513 | Breast | IDC | nucleobase-containing compound catabolic process | 47/1434 | 407/18723 | 3.12e-03 | 2.63e-02 | 47 |
| GO:004427012 | Breast | IDC | cellular nitrogen compound catabolic process | 50/1434 | 451/18723 | 5.29e-03 | 3.93e-02 | 50 |
| 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 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 |
| 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 |
| SET | SNV | Missense_Mutation | rs142648600 | c.548N>T | p.Ser183Leu | p.S183L | Q01105 | protein_coding | tolerated(0.16) | benign(0.11) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SET | SNV | Missense_Mutation | novel | c.270N>C | p.Lys90Asn | p.K90N | Q01105 | protein_coding | tolerated(0.05) | benign(0.16) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SET | SNV | Missense_Mutation | c.195N>C | p.Glu65Asp | p.E65D | Q01105 | protein_coding | deleterious(0.01) | possibly_damaging(0.651) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD | |
| SET | SNV | Missense_Mutation | novel | c.469N>A | p.His157Asn | p.H157N | Q01105 | protein_coding | tolerated(0.06) | benign(0.208) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| SET | SNV | Missense_Mutation | c.229C>T | p.Arg77Cys | p.R77C | Q01105 | protein_coding | tolerated(0.11) | benign(0.444) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| SET | SNV | Missense_Mutation | c.572G>A | p.Ser191Asn | p.S191N | Q01105 | protein_coding | tolerated(0.16) | benign(0.029) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| SET | SNV | Missense_Mutation | c.260N>C | p.Leu87Ser | p.L87S | Q01105 | protein_coding | deleterious(0) | probably_damaging(0.974) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SET | SNV | Missense_Mutation | c.508N>A | p.Glu170Lys | p.E170K | Q01105 | protein_coding | tolerated(0.18) | benign(0.086) | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| SET | deletion | Frame_Shift_Del | c.273delN | p.Pro92GlnfsTer5 | p.P92Qfs*5 | Q01105 | protein_coding | TCGA-CM-5862-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |||
| SET | SNV | Missense_Mutation | novel | c.161N>C | p.Glu54Ala | p.E54A | Q01105 | protein_coding | tolerated(0.06) | possibly_damaging(0.893) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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