Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Center for Computational Systems Medicine
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Gene summary

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Malignant transformation analysis

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Malignant transformation related pathway analysis

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Cell-cell communication analysis

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Single-cell gene regulatory network inference analysis

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Somatic mutation of malignant transformation related genes

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Related drugs of malignant transformation related genes

Gene: SETX

Gene summary for SETX

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SETX

Gene ID

23064

Gene namesenataxin
Gene AliasALS4
Cytomap9q34.13
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

Q7Z333


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Malignant transformation analysis

check button 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
check button Malignant transformation involving gene list.
Entrez IDSymbolReplicatesSpeciesOrganTissueAdj P-valueLog2FCMalignancy
23064SETXCA_HPV_1HumanCervixCC1.46e-051.81e-010.0264
23064SETXCCI_1HumanCervixCC2.62e-035.60e-010.528
23064SETXCCI_2HumanCervixCC2.99e-151.75e+000.5249
23064SETXCCI_3HumanCervixCC3.06e-169.89e-010.516
23064SETXHTA11_3410_2000001011HumanColorectumAD1.23e-05-4.08e-010.0155
23064SETXHTA11_866_3004761011HumanColorectumAD4.60e-02-4.13e-010.096
23064SETXHTA11_7696_3000711011HumanColorectumAD3.52e-08-4.28e-010.0674
23064SETXHTA11_99999974143_84620HumanColorectumMSS3.77e-07-4.30e-010.3005
23064SETXA002-C-010HumanColorectumFAP6.06e-04-1.30e-010.242
23064SETXA015-C-203HumanColorectumFAP1.07e-24-2.12e-01-0.1294
23064SETXA015-C-204HumanColorectumFAP4.63e-03-5.04e-02-0.0228
23064SETXA014-C-040HumanColorectumFAP6.55e-03-3.18e-01-0.1184
23064SETXA002-C-201HumanColorectumFAP3.30e-08-8.87e-020.0324
23064SETXA002-C-203HumanColorectumFAP3.86e-03-1.37e-010.2786
23064SETXA001-C-119HumanColorectumFAP1.76e-03-4.88e-02-0.1557
23064SETXA001-C-108HumanColorectumFAP1.99e-159.67e-02-0.0272
23064SETXA002-C-205HumanColorectumFAP2.20e-17-5.64e-02-0.1236
23064SETXA001-C-104HumanColorectumFAP4.62e-031.50e-010.0184
23064SETXA015-C-005HumanColorectumFAP3.69e-03-5.12e-02-0.0336
23064SETXA015-C-006HumanColorectumFAP6.83e-12-5.72e-02-0.0994
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
CervixThe image shows the 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.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)The image shows the 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.FAP: Familial adenomatous polyposis
CRC: Colorectal cancer
Colorectum (HTA11)The image shows the 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.AD: Adenomas
SER: Sessile serrated lesions
MSI-H: Microsatellite-high colorectal cancer
MSS: Microsatellite stable colorectal cancer
EsophagusThe image shows the 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.ESCC: Esophageal squamous cell carcinoma
HGIN: High-grade intraepithelial neoplasias
LGIN: Low-grade intraepithelial neoplasias
LiverThe image shows the 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.HCC: Hepatocellular carcinoma
NAFLD: Non-alcoholic fatty liver disease
LungThe image shows the 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.AAH: Atypical adenomatous hyperplasia
AIS: Adenocarcinoma in situ
IAC: Invasive lung adenocarcinoma
MIA: Minimally invasive adenocarcinoma
Oral CavityThe image shows the 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.EOLP: Erosive Oral lichen planus
LP: leukoplakia
NEOLP: Non-erosive oral lichen planus
OSCC: Oral squamous cell carcinoma
ProstateThe image shows the 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.BPH: Benign Prostatic Hyperplasia
SkinThe image shows the 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.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
ThyroidThe image shows the 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.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

check buttonFind out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
check button Figure of enriched GO biological processes.
TissueDisease StageEnriched GO biological Processes
ColorectumADGO analysis - Figure of enriched GO biological processes: 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).
ColorectumSERGO analysis - Figure of enriched GO biological processes: 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).
ColorectumMSSGO analysis - Figure of enriched GO biological processes: 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).
ColorectumMSI-HGO analysis - Figure of enriched GO biological processes: 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).
ColorectumFAPGO analysis - Figure of enriched GO biological processes: 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).
∗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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check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:00485114ColorectumCRCrhythmic process64/2078298/187231.43e-071.62e-0564
GO:00003775ColorectumCRCRNA splicing, via transesterification reactions with bulged adenosine as nucleophile66/2078320/187234.39e-073.37e-0566
GO:00003985ColorectumCRCmRNA splicing, via spliceosome66/2078320/187234.39e-073.37e-0566
GO:00003755ColorectumCRCRNA splicing, via transesterification reactions66/2078324/187237.00e-074.61e-0566
GO:00076234ColorectumCRCcircadian rhythm47/2078210/187231.89e-069.29e-0547
GO:00109754ColorectumCRCregulation of neuron projection development82/2078445/187232.51e-061.19e-0482
GO:00226185ColorectumCRCribonucleoprotein complex assembly48/2078220/187233.16e-061.44e-0448
GO:00718265ColorectumCRCribonucleoprotein complex subunit organization49/2078227/187233.44e-061.51e-0449
GO:00313464ColorectumCRCpositive regulation of cell projection organization67/2078353/187237.45e-062.72e-0467
GO:00621975ColorectumCRCcellular response to chemical stress63/2078337/187232.24e-056.49e-0463
GO:00329845ColorectumCRCprotein-containing complex disassembly46/2078224/187232.61e-057.18e-0446
GO:00224115ColorectumCRCcellular component disassembly75/2078443/187231.26e-042.42e-0375
GO:00345995ColorectumCRCcellular response to oxidative stress53/2078288/187231.47e-042.68e-0353
GO:00226135ColorectumCRCribonucleoprotein complex biogenesis76/2078463/187233.04e-044.78e-0376
GO:00069795ColorectumCRCresponse to oxidative stress73/2078446/187234.31e-046.34e-0373
GO:00425425ColorectumCRCresponse to hydrogen peroxide30/2078146/187236.12e-048.15e-0330
GO:00003025ColorectumCRCresponse to reactive oxygen species41/2078222/187237.28e-049.35e-0341
GO:00432443ColorectumCRCregulation of protein-containing complex disassembly25/2078121/187231.54e-031.63e-0225
GO:00002453ColorectumCRCspliceosomal complex assembly17/207879/187235.34e-034.05e-0217
GO:000838026EsophagusHGINRNA splicing160/2587434/187233.74e-341.12e-30160
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0501418CervixCCAmyotrophic lateral sclerosis103/1267364/84651.79e-114.47e-102.64e-10103
hsa0501419CervixCCAmyotrophic lateral sclerosis103/1267364/84651.79e-114.47e-102.64e-10103
hsa05014ColorectumADAmyotrophic lateral sclerosis164/2092364/84654.28e-181.27e-168.09e-17164
hsa050141ColorectumADAmyotrophic lateral sclerosis164/2092364/84654.28e-181.27e-168.09e-17164
hsa050148ColorectumFAPAmyotrophic lateral sclerosis91/1404364/84651.84e-052.36e-041.44e-0491
hsa050149ColorectumFAPAmyotrophic lateral sclerosis91/1404364/84651.84e-052.36e-041.44e-0491
hsa0501430EsophagusHGINAmyotrophic lateral sclerosis140/1383364/84652.13e-251.16e-239.19e-24140
hsa05014113EsophagusHGINAmyotrophic lateral sclerosis140/1383364/84652.13e-251.16e-239.19e-24140
hsa05014210EsophagusESCCAmyotrophic lateral sclerosis266/4205364/84651.31e-202.20e-181.13e-18266
hsa0501438EsophagusESCCAmyotrophic lateral sclerosis266/4205364/84651.31e-202.20e-181.13e-18266
hsa0501422LiverHCCAmyotrophic lateral sclerosis252/4020364/84658.85e-187.41e-164.12e-16252
hsa0501432LiverHCCAmyotrophic lateral sclerosis252/4020364/84658.85e-187.41e-164.12e-16252
hsa0501428Oral cavityOSCCAmyotrophic lateral sclerosis246/3704364/84656.65e-211.11e-185.67e-19246
hsa05014112Oral cavityOSCCAmyotrophic lateral sclerosis246/3704364/84656.65e-211.11e-185.67e-19246
hsa0501445Oral cavityEOLPAmyotrophic lateral sclerosis93/1218364/84657.07e-091.14e-076.74e-0893
hsa0501455Oral cavityEOLPAmyotrophic lateral sclerosis93/1218364/84657.07e-091.14e-076.74e-0893
hsa0501462Oral cavityNEOLPAmyotrophic lateral sclerosis95/1112364/84658.76e-123.98e-102.50e-1095
hsa0501472Oral cavityNEOLPAmyotrophic lateral sclerosis95/1112364/84658.76e-123.98e-102.50e-1095
hsa0501426ProstateBPHAmyotrophic lateral sclerosis151/1718364/84653.37e-211.01e-196.25e-20151
hsa05014111ProstateBPHAmyotrophic lateral sclerosis151/1718364/84653.37e-211.01e-196.25e-20151
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Cell-cell communication analysis

check buttonIdentification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states
LigandReceptorLRpairPathwayTissueDisease Stage
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Single-cell gene regulatory network inference analysis

check buttonFind out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states
TFCell TypeTissueDisease StageTarget GeneRSSRegulon 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

check buttonAnnotation of somatic variants for genes involved in malignant transformation
Hugo SymbolVariant ClassVariant ClassificationdbSNP RSHGVScHGVSpHGVSp ShortSWISSPROTBIOTYPESIFTPolyPhenTumor Sample BarcodeTissueHistologySexAgeStageTherapy TypesDrugsOutcome
SETXSNVMissense_Mutationrs757652780c.5566G>Ap.Glu1856Lysp.E1856KQ7Z333protein_codingdeleterious(0.05)probably_damaging(0.994)TCGA-A2-A0EY-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
SETXSNVMissense_Mutationc.3961G>Ap.Asp1321Asnp.D1321NQ7Z333protein_codingtolerated(0.21)benign(0.007)TCGA-A2-A0EY-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
SETXSNVMissense_Mutationc.2356G>Cp.Glu786Glnp.E786QQ7Z333protein_codingdeleterious_low_confidence(0.04)possibly_damaging(0.69)TCGA-A2-A0YK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
SETXSNVMissense_Mutationnovelc.7568N>Ap.Thr2523Asnp.T2523NQ7Z333protein_codingtolerated(0.16)benign(0.188)TCGA-A2-A4S1-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SETXSNVMissense_Mutationc.689N>Gp.Asp230Glyp.D230GQ7Z333protein_codingdeleterious(0)probably_damaging(0.914)TCGA-A8-A07P-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapy5-fluorouracilSD
SETXSNVMissense_Mutationc.5126N>Cp.Lys1709Thrp.K1709TQ7Z333protein_codingtolerated(0.8)benign(0.123)TCGA-A8-A094-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SETXSNVMissense_Mutationc.6590N>Gp.His2197Argp.H2197RQ7Z333protein_codingdeleterious(0)probably_damaging(0.956)TCGA-A8-A09N-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
SETXSNVMissense_Mutationnovelc.7393N>Ap.Leu2465Ilep.L2465IQ7Z333protein_codingtolerated(0.05)possibly_damaging(0.749)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SETXSNVMissense_Mutationnovelc.7034N>Cp.Ile2345Thrp.I2345TQ7Z333protein_codingdeleterious(0)probably_damaging(0.998)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SETXSNVMissense_Mutationnovelc.6252N>Tp.Lys2084Asnp.K2084NQ7Z333protein_codingdeleterious(0)probably_damaging(0.999)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
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Related drugs of malignant transformation related genes

check buttonIdentification of chemicals and drugs interact with genes involved in malignant transfromation
(DGIdb 4.0)
Entrez IDSymbolCategoryInteraction TypesDrug Claim NameDrug NamePMIDs
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