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Gene: SETX |
Gene summary for SETX |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SETX | Gene ID | 23064 |
| Gene name | senataxin | |
| Gene Alias | ALS4 | |
| Cytomap | 9q34.13 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q7Z333 |
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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 |
| 23064 | SETX | CA_HPV_1 | Human | Cervix | CC | 1.46e-05 | 1.81e-01 | 0.0264 |
| 23064 | SETX | CCI_1 | Human | Cervix | CC | 2.62e-03 | 5.60e-01 | 0.528 |
| 23064 | SETX | CCI_2 | Human | Cervix | CC | 2.99e-15 | 1.75e+00 | 0.5249 |
| 23064 | SETX | CCI_3 | Human | Cervix | CC | 3.06e-16 | 9.89e-01 | 0.516 |
| 23064 | SETX | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.23e-05 | -4.08e-01 | 0.0155 |
| 23064 | SETX | HTA11_866_3004761011 | Human | Colorectum | AD | 4.60e-02 | -4.13e-01 | 0.096 |
| 23064 | SETX | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.52e-08 | -4.28e-01 | 0.0674 |
| 23064 | SETX | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.77e-07 | -4.30e-01 | 0.3005 |
| 23064 | SETX | A002-C-010 | Human | Colorectum | FAP | 6.06e-04 | -1.30e-01 | 0.242 |
| 23064 | SETX | A015-C-203 | Human | Colorectum | FAP | 1.07e-24 | -2.12e-01 | -0.1294 |
| 23064 | SETX | A015-C-204 | Human | Colorectum | FAP | 4.63e-03 | -5.04e-02 | -0.0228 |
| 23064 | SETX | A014-C-040 | Human | Colorectum | FAP | 6.55e-03 | -3.18e-01 | -0.1184 |
| 23064 | SETX | A002-C-201 | Human | Colorectum | FAP | 3.30e-08 | -8.87e-02 | 0.0324 |
| 23064 | SETX | A002-C-203 | Human | Colorectum | FAP | 3.86e-03 | -1.37e-01 | 0.2786 |
| 23064 | SETX | A001-C-119 | Human | Colorectum | FAP | 1.76e-03 | -4.88e-02 | -0.1557 |
| 23064 | SETX | A001-C-108 | Human | Colorectum | FAP | 1.99e-15 | 9.67e-02 | -0.0272 |
| 23064 | SETX | A002-C-205 | Human | Colorectum | FAP | 2.20e-17 | -5.64e-02 | -0.1236 |
| 23064 | SETX | A001-C-104 | Human | Colorectum | FAP | 4.62e-03 | 1.50e-01 | 0.0184 |
| 23064 | SETX | A015-C-005 | Human | Colorectum | FAP | 3.69e-03 | -5.12e-02 | -0.0336 |
| 23064 | SETX | A015-C-006 | Human | Colorectum | FAP | 6.83e-12 | -5.72e-02 | -0.0994 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| 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 |
| 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:000697910 | Cervix | CC | response to oxidative stress | 102/2311 | 446/18723 | 2.99e-10 | 4.36e-08 | 102 |
| GO:000030210 | Cervix | CC | response to reactive oxygen species | 56/2311 | 222/18723 | 1.00e-07 | 5.25e-06 | 56 |
| GO:006219710 | Cervix | CC | cellular response to chemical stress | 76/2311 | 337/18723 | 1.01e-07 | 5.25e-06 | 76 |
| GO:004348410 | Cervix | CC | regulation of RNA splicing | 42/2311 | 148/18723 | 1.25e-07 | 6.24e-06 | 42 |
| GO:004254210 | Cervix | CC | response to hydrogen peroxide | 40/2311 | 146/18723 | 6.79e-07 | 2.46e-05 | 40 |
| GO:00485118 | Cervix | CC | rhythmic process | 65/2311 | 298/18723 | 2.79e-06 | 8.04e-05 | 65 |
| GO:003459910 | Cervix | CC | cellular response to oxidative stress | 63/2311 | 288/18723 | 3.58e-06 | 9.50e-05 | 63 |
| GO:00109757 | Cervix | CC | regulation of neuron projection development | 88/2311 | 445/18723 | 4.26e-06 | 1.09e-04 | 88 |
| GO:00313467 | Cervix | CC | positive regulation of cell projection organization | 72/2311 | 353/18723 | 1.04e-05 | 2.32e-04 | 72 |
| GO:002261310 | Cervix | CC | ribonucleoprotein complex biogenesis | 88/2311 | 463/18723 | 2.11e-05 | 3.82e-04 | 88 |
| GO:002261810 | Cervix | CC | ribonucleoprotein complex assembly | 49/2311 | 220/18723 | 2.52e-05 | 4.29e-04 | 49 |
| GO:007182610 | Cervix | CC | ribonucleoprotein complex subunit organization | 49/2311 | 227/18723 | 5.91e-05 | 8.54e-04 | 49 |
| GO:002241110 | Cervix | CC | cellular component disassembly | 83/2311 | 443/18723 | 6.04e-05 | 8.68e-04 | 83 |
| GO:00076238 | Cervix | CC | circadian rhythm | 46/2311 | 210/18723 | 6.76e-05 | 9.60e-04 | 46 |
| GO:003461410 | Cervix | CC | cellular response to reactive oxygen species | 35/2311 | 155/18723 | 2.59e-04 | 2.85e-03 | 35 |
| GO:00331208 | Cervix | CC | positive regulation of RNA splicing | 13/2311 | 37/18723 | 2.99e-04 | 3.21e-03 | 13 |
| GO:00434913 | Cervix | CC | protein kinase B signaling | 43/2311 | 211/18723 | 5.95e-04 | 5.60e-03 | 43 |
| GO:000838010 | Cervix | CC | RNA splicing | 76/2311 | 434/18723 | 9.79e-04 | 8.19e-03 | 76 |
| GO:00323923 | Cervix | CC | DNA geometric change | 21/2311 | 90/18723 | 2.71e-03 | 1.85e-02 | 21 |
| GO:00329847 | Cervix | CC | protein-containing complex disassembly | 41/2311 | 224/18723 | 6.13e-03 | 3.48e-02 | 41 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501427 | Prostate | Tumor | Amyotrophic lateral sclerosis | 155/1791 | 364/8465 | 3.41e-21 | 1.13e-19 | 6.99e-20 | 155 |
| hsa0501436 | Prostate | Tumor | Amyotrophic lateral sclerosis | 155/1791 | 364/8465 | 3.41e-21 | 1.13e-19 | 6.99e-20 | 155 |
| 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 |
| SETX | SNV | Missense_Mutation | rs757652780 | c.5566G>A | p.Glu1856Lys | p.E1856K | Q7Z333 | protein_coding | deleterious(0.05) | probably_damaging(0.994) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| SETX | SNV | Missense_Mutation | c.3961G>A | p.Asp1321Asn | p.D1321N | Q7Z333 | protein_coding | tolerated(0.21) | benign(0.007) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SETX | SNV | Missense_Mutation | c.2356G>C | p.Glu786Gln | p.E786Q | Q7Z333 | protein_coding | deleterious_low_confidence(0.04) | possibly_damaging(0.69) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| SETX | SNV | Missense_Mutation | novel | c.7568N>A | p.Thr2523Asn | p.T2523N | Q7Z333 | protein_coding | tolerated(0.16) | benign(0.188) | TCGA-A2-A4S1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SETX | SNV | Missense_Mutation | c.689N>G | p.Asp230Gly | p.D230G | Q7Z333 | protein_coding | deleterious(0) | probably_damaging(0.914) | TCGA-A8-A07P-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
| SETX | SNV | Missense_Mutation | c.5126N>C | p.Lys1709Thr | p.K1709T | Q7Z333 | protein_coding | tolerated(0.8) | benign(0.123) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SETX | SNV | Missense_Mutation | c.6590N>G | p.His2197Arg | p.H2197R | Q7Z333 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-A8-A09N-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| SETX | SNV | Missense_Mutation | novel | c.7393N>A | p.Leu2465Ile | p.L2465I | Q7Z333 | protein_coding | tolerated(0.05) | possibly_damaging(0.749) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SETX | SNV | Missense_Mutation | novel | c.7034N>C | p.Ile2345Thr | p.I2345T | Q7Z333 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SETX | SNV | Missense_Mutation | novel | c.6252N>T | p.Lys2084Asn | p.K2084N | Q7Z333 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| 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 |
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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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