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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501418 | Cervix | CC | Amyotrophic lateral sclerosis | 103/1267 | 364/8465 | 1.79e-11 | 4.47e-10 | 2.64e-10 | 103 |
hsa0501419 | Cervix | CC | Amyotrophic lateral sclerosis | 103/1267 | 364/8465 | 1.79e-11 | 4.47e-10 | 2.64e-10 | 103 |
hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa050148 | Colorectum | FAP | Amyotrophic lateral sclerosis | 91/1404 | 364/8465 | 1.84e-05 | 2.36e-04 | 1.44e-04 | 91 |
hsa050149 | Colorectum | FAP | Amyotrophic lateral sclerosis | 91/1404 | 364/8465 | 1.84e-05 | 2.36e-04 | 1.44e-04 | 91 |
hsa0501430 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
hsa05014113 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
hsa0501422 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
hsa0501432 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
hsa0501428 | Oral cavity | OSCC | Amyotrophic lateral sclerosis | 246/3704 | 364/8465 | 6.65e-21 | 1.11e-18 | 5.67e-19 | 246 |
hsa05014112 | Oral cavity | OSCC | Amyotrophic lateral sclerosis | 246/3704 | 364/8465 | 6.65e-21 | 1.11e-18 | 5.67e-19 | 246 |
hsa0501445 | Oral cavity | EOLP | Amyotrophic lateral sclerosis | 93/1218 | 364/8465 | 7.07e-09 | 1.14e-07 | 6.74e-08 | 93 |
hsa0501455 | Oral cavity | EOLP | Amyotrophic lateral sclerosis | 93/1218 | 364/8465 | 7.07e-09 | 1.14e-07 | 6.74e-08 | 93 |
hsa0501462 | Oral cavity | NEOLP | Amyotrophic lateral sclerosis | 95/1112 | 364/8465 | 8.76e-12 | 3.98e-10 | 2.50e-10 | 95 |
hsa0501472 | Oral cavity | NEOLP | Amyotrophic lateral sclerosis | 95/1112 | 364/8465 | 8.76e-12 | 3.98e-10 | 2.50e-10 | 95 |
hsa0501426 | Prostate | BPH | Amyotrophic lateral sclerosis | 151/1718 | 364/8465 | 3.37e-21 | 1.01e-19 | 6.25e-20 | 151 |
hsa05014111 | Prostate | BPH | Amyotrophic lateral sclerosis | 151/1718 | 364/8465 | 3.37e-21 | 1.01e-19 | 6.25e-20 | 151 |
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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 |
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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. |
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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 | novel | c.3856A>C | p.Lys1286Gln | p.K1286Q | Q7Z333 | protein_coding | deleterious(0) | possibly_damaging(0.532) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
SETX | SNV | Missense_Mutation | rs143270460 | c.1066G>A | p.Val356Ile | p.V356I | Q7Z333 | protein_coding | deleterious(0.04) | probably_damaging(0.992) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
SETX | SNV | Missense_Mutation | rs369919717 | c.7019N>A | p.Arg2340Gln | p.R2340Q | Q7Z333 | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
SETX | SNV | Missense_Mutation | c.4946N>A | p.Val1649Asp | p.V1649D | Q7Z333 | protein_coding | deleterious(0.02) | benign(0.276) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SETX | SNV | Missense_Mutation | c.124N>C | p.Glu42Gln | p.E42Q | Q7Z333 | protein_coding | deleterious(0.03) | possibly_damaging(0.745) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SETX | SNV | Missense_Mutation | c.7259N>G | p.Phe2420Cys | p.F2420C | Q7Z333 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-CM-4744-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SETX | SNV | Missense_Mutation | c.1744N>T | p.His582Tyr | p.H582Y | Q7Z333 | protein_coding | deleterious(0.01) | benign(0.335) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
SETX | SNV | Missense_Mutation | rs771341212 | c.896N>A | p.Arg299His | p.R299H | Q7Z333 | protein_coding | deleterious(0.02) | probably_damaging(0.974) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SETX | SNV | Missense_Mutation | c.415C>T | p.Arg139Trp | p.R139W | Q7Z333 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SETX | SNV | Missense_Mutation | novel | c.4579N>T | p.Asp1527Tyr | p.D1527Y | Q7Z333 | protein_coding | deleterious(0.02) | benign(0.001) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <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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