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: GTF3A

Gene summary for GTF3A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

GTF3A

Gene ID

2971

Gene namegeneral transcription factor IIIA
Gene AliasAP2
Cytomap13q12.2
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

Q92664


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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
2971GTF3ACA_HPV_1HumanCervixCC5.54e-03-4.39e-020.0264
2971GTF3AN_HPV_2HumanCervixN_HPV2.18e-03-1.04e-02-0.0131
2971GTF3ACCI_1HumanCervixCC1.79e-04-5.03e-010.528
2971GTF3ACCI_3HumanCervixCC8.84e-03-4.13e-010.516
2971GTF3ACCII_1HumanCervixCC9.95e-12-5.41e-010.3249
2971GTF3ATumorHumanCervixCC2.37e-02-2.87e-010.1241
2971GTF3Asample3HumanCervixCC3.61e-07-3.26e-010.1387
2971GTF3AL1HumanCervixCC1.83e-02-1.37e-010.0802
2971GTF3AT3HumanCervixCC3.57e-10-3.75e-010.1389
2971GTF3AHTA11_78_2000001011HumanColorectumAD3.56e-023.20e-01-0.1088
2971GTF3AHTA11_7696_3000711011HumanColorectumAD3.37e-031.97e-010.0674
2971GTF3AHTA11_99999970781_79442HumanColorectumMSS2.02e-042.68e-010.294
2971GTF3AHTA11_99999965104_69814HumanColorectumMSS5.72e-249.72e-010.281
2971GTF3AHTA11_99999971662_82457HumanColorectumMSS2.15e-551.34e+000.3859
2971GTF3AHTA11_99999973899_84307HumanColorectumMSS8.61e-148.64e-010.2585
2971GTF3AHTA11_99999974143_84620HumanColorectumMSS9.07e-042.73e-010.3005
2971GTF3ACRC-1-8810HumanColorectumCRC1.37e-196.01e-010.6257
2971GTF3AAEH-subject1HumanEndometriumAEH7.20e-16-3.60e-01-0.3059
2971GTF3AAEH-subject2HumanEndometriumAEH3.10e-08-3.34e-01-0.2525
2971GTF3AAEH-subject3HumanEndometriumAEH8.78e-09-2.35e-01-0.2576
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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
EndometriumThe 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid 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
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:004227310CervixCCribosomal large subunit biogenesis26/231172/187231.87e-078.48e-0626
GO:002261310CervixCCribonucleoprotein complex biogenesis88/2311463/187232.11e-053.82e-0488
GO:004225410CervixCCribosome biogenesis62/2311299/187232.48e-054.27e-0462
GO:002261325CervixN_HPVribonucleoprotein complex biogenesis30/534463/187232.78e-057.49e-0430
GO:004225424CervixN_HPVribosome biogenesis21/534299/187231.46e-042.68e-0321
GO:0022613ColorectumADribonucleoprotein complex biogenesis151/3918463/187231.96e-091.39e-07151
GO:0042273ColorectumADribosomal large subunit biogenesis28/391872/187233.74e-044.31e-0328
GO:0042254ColorectumADribosome biogenesis84/3918299/187231.82e-031.50e-0284
GO:00226132ColorectumMSSribonucleoprotein complex biogenesis144/3467463/187232.76e-113.67e-09144
GO:00422732ColorectumMSSribosomal large subunit biogenesis28/346772/187234.16e-057.83e-0428
GO:00422542ColorectumMSSribosome biogenesis79/3467299/187234.32e-045.23e-0379
GO:00226135ColorectumCRCribonucleoprotein complex biogenesis76/2078463/187233.04e-044.78e-0376
GO:002261316EndometriumAEHribonucleoprotein complex biogenesis107/2100463/187231.43e-134.08e-11107
GO:004227316EndometriumAEHribosomal large subunit biogenesis30/210072/187233.69e-115.03e-0930
GO:004225416EndometriumAEHribosome biogenesis67/2100299/187231.95e-081.18e-0667
GO:002261317EndometriumEECribonucleoprotein complex biogenesis108/2168463/187234.60e-139.86e-11108
GO:004227317EndometriumEECribosomal large subunit biogenesis30/216872/187238.19e-111.07e-0830
GO:004225417EndometriumEECribosome biogenesis68/2168299/187232.90e-081.68e-0668
GO:002261327EsophagusHGINribonucleoprotein complex biogenesis158/2587463/187232.61e-295.23e-26158
GO:004225426EsophagusHGINribosome biogenesis101/2587299/187238.74e-194.03e-16101
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
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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
GTF3AMSCLiverHealthyTMSB10,UNC5B,CTSZ, etc.1.98e-02The 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.
GTF3AMVALiverNAFLDTMSB10,UNC5B,CTSZ, etc.3.19e-02The 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.
GTF3AAT1LungIACRAC1,RPS3A,BRI3, etc.8.99e-02The 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.
GTF3ASPIOral cavityADJRPL21,SMIM19,ZDHHC4, etc.6.42e-02The 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.
GTF3ASPIOral cavityLPRPL21,SMIM19,ZDHHC4, etc.3.39e-01The 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.
GTF3APLAOral cavityOSCCGYPC,RASGRP2,SEC11C, etc.1.45e-01The 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.
GTF3ASMCOral cavityADJPGAM2,PDE4DIP,CKM, etc.3.33e-01The 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.
GTF3APVAOral cavityNEOLPPGAM2,PDE4DIP,CKM, etc.3.89e-02The 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.
GTF3ACHIEFStomachCAG with IMDOK1,DNAJC27-AS1,STBD1, etc.5.10e-01The 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.
GTF3ACHIEFStomachSIMDOK1,DNAJC27-AS1,STBD1, etc.1.19e-01The 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.
∗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
GTF3ASNVMissense_Mutationc.974N>Gp.Leu325Argp.L325RQ92664protein_codingdeleterious(0)probably_damaging(0.987)TCGA-A6-5661-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
GTF3ASNVMissense_Mutationc.569N>Cp.Val190Alap.V190AQ92664protein_codingtolerated(0.97)benign(0.001)TCGA-A6-A565-01Colorectumcolon adenocarcinomaFemale<65III/IVUnspecific5FUPD
GTF3ASNVMissense_Mutationnovelc.304T>Ap.Cys102Serp.C102SQ92664protein_codingdeleterious(0)probably_damaging(1)TCGA-AA-3858-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
GTF3ASNVMissense_Mutationnovelc.664N>Cp.Cys222Argp.C222RQ92664protein_codingdeleterious(0)probably_damaging(1)TCGA-AA-3947-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
GTF3ASNVMissense_Mutationnovelc.918G>Tp.Lys306Asnp.K306NQ92664protein_codingdeleterious(0.01)possibly_damaging(0.777)TCGA-AA-A010-01Colorectumcolon adenocarcinomaFemale<65I/IIChemotherapyfolinicCR
GTF3ASNVMissense_Mutationrs758878764c.683G>Ap.Arg228Hisp.R228HQ92664protein_codingtolerated(0.12)benign(0.168)TCGA-D5-6926-01Colorectumcolon adenocarcinomaMale>=65III/IVChemotherapy5-fluorouracilSD
GTF3ASNVMissense_Mutationnovelc.918N>Tp.Lys306Asnp.K306NQ92664protein_codingdeleterious(0.01)possibly_damaging(0.777)TCGA-AG-3892-01Colorectumrectum adenocarcinomaFemale<65I/IIUnknownUnknownSD
GTF3ASNVMissense_Mutationc.824N>Ap.Arg275Hisp.R275HQ92664protein_codingdeleterious(0.02)benign(0.249)TCGA-A5-A0G1-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
GTF3ASNVMissense_Mutationrs758878764c.683N>Ap.Arg228Hisp.R228HQ92664protein_codingtolerated(0.12)benign(0.168)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
GTF3ASNVMissense_Mutationnovelc.817N>Ap.Glu273Lysp.E273KQ92664protein_codingtolerated(0.12)possibly_damaging(0.894)TCGA-AX-A2HC-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapypaclitaxelPD
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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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