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: RFX3

Gene summary for RFX3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RFX3

Gene ID

5991

Gene nameregulatory factor X3
Gene AliasRFX3
Cytomap9p24.2
Gene Typeprotein-coding
GO ID

GO:0001539

UniProtAcc

P48380


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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
5991RFX3CCI_1HumanCervixCC1.02e-034.93e-010.528
5991RFX3CCI_2HumanCervixCC4.39e-141.18e+000.5249
5991RFX3CCI_3HumanCervixCC9.58e-281.13e+000.516
5991RFX3HTA11_3410_2000001011HumanColorectumAD1.56e-15-5.82e-010.0155
5991RFX3HTA11_2487_2000001011HumanColorectumSER1.55e-04-5.44e-01-0.1808
5991RFX3HTA11_2951_2000001011HumanColorectumAD3.07e-02-7.52e-010.0216
5991RFX3HTA11_1938_2000001011HumanColorectumAD1.22e-02-2.92e-01-0.0811
5991RFX3HTA11_78_2000001011HumanColorectumAD1.90e-03-3.58e-01-0.1088
5991RFX3HTA11_3361_2000001011HumanColorectumAD1.55e-07-6.85e-01-0.1207
5991RFX3HTA11_696_2000001011HumanColorectumAD6.32e-07-4.27e-01-0.1464
5991RFX3HTA11_866_2000001011HumanColorectumAD2.14e-12-4.92e-01-0.1001
5991RFX3HTA11_866_3004761011HumanColorectumAD2.19e-02-4.53e-010.096
5991RFX3HTA11_8622_2000001021HumanColorectumSER2.83e-03-6.57e-010.0528
5991RFX3HTA11_10711_2000001011HumanColorectumAD2.75e-08-6.07e-010.0338
5991RFX3HTA11_7696_3000711011HumanColorectumAD4.47e-13-4.94e-010.0674
5991RFX3HTA11_6818_2000001011HumanColorectumAD4.83e-03-6.37e-010.0112
5991RFX3HTA11_99999970781_79442HumanColorectumMSS7.28e-04-3.10e-010.294
5991RFX3HTA11_99999965062_69753HumanColorectumMSI-H2.36e-037.90e-010.3487
5991RFX3HTA11_99999971662_82457HumanColorectumMSS6.07e-03-3.48e-010.3859
5991RFX3HTA11_99999973899_84307HumanColorectumMSS6.11e-04-6.06e-010.2585
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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
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
∗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:00107206CervixCCpositive regulation of cell development64/2311298/187235.69e-061.41e-0464
GO:00308563CervixCCregulation of epithelial cell differentiation36/2311154/187231.02e-041.31e-0336
GO:000206410CervixCCepithelial cell development45/2311220/187234.14e-044.21e-0345
GO:00158337CervixCCpeptide transport46/2311264/187239.69e-034.78e-0246
GO:0002064ColorectumADepithelial cell development89/3918220/187232.98e-113.52e-0989
GO:0050708ColorectumADregulation of protein secretion83/3918268/187236.59e-051.07e-0383
GO:0009306ColorectumADprotein secretion105/3918359/187231.05e-041.57e-03105
GO:0035592ColorectumADestablishment of protein localization to extracellular region105/3918360/187231.18e-041.73e-03105
GO:0071692ColorectumADprotein localization to extracellular region106/3918368/187231.86e-042.49e-03106
GO:0050796ColorectumADregulation of insulin secretion54/3918165/187232.60e-043.25e-0354
GO:0010720ColorectumADpositive regulation of cell development87/3918298/187234.17e-044.71e-0387
GO:0030073ColorectumADinsulin secretion61/3918195/187234.28e-044.81e-0361
GO:0015833ColorectumADpeptide transport77/3918264/187238.90e-048.60e-0377
GO:0090087ColorectumADregulation of peptide transport60/3918202/187231.94e-031.58e-0260
GO:0030072ColorectumADpeptide hormone secretion68/3918236/187232.39e-031.85e-0268
GO:0002791ColorectumADregulation of peptide secretion59/3918200/187232.50e-031.92e-0259
GO:0090276ColorectumADregulation of peptide hormone secretion58/3918196/187232.51e-031.92e-0258
GO:0002790ColorectumADpeptide secretion69/3918242/187232.97e-032.22e-0269
GO:0042886ColorectumADamide transport83/3918301/187233.37e-032.46e-0283
GO:00020641ColorectumSERepithelial cell development64/2897220/187231.96e-071.10e-0564
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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
RFX3FIBBreastADJMIR181A1HG,ANKRD42,ANKRD44, etc.5.02e-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.
RFX3CD8TEXPEndometriumADJZBTB20,SIK3,ARHGAP15, etc.2.48e-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.
RFX3BMEMEndometriumEECZBTB20,SIK3,ARHGAP15, etc.1.22e-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.
RFX3TH17EndometriumEECZBTB20,SIK3,ARHGAP15, etc.5.09e-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.
RFX3CD8TEXPEndometriumEECZBTB20,SIK3,ARHGAP15, etc.1.31e-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.
RFX3TREGLungADJARHGAP15,SIK3,ZBTB20, etc.8.52e-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.
RFX3CD4TNLungADJARHGAP15,SIK3,ZBTB20, 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.
RFX3PANINPancreasADJRFX2,LRRIQ1,EFCAB2, etc.6.24e-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.
RFX3CD4TNSkinADJJUND,ZBTB20,SIK3, etc.1.94e-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.
RFX3CD8TEXPSkincSCCJUND,ZBTB20,SIK3, etc.1.49e-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
RFX3SNVMissense_Mutationnovelc.1490N>Ap.Arg497Glnp.R497QP48380protein_codingdeleterious(0.02)possibly_damaging(0.639)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RFX3SNVMissense_Mutationc.209N>Ap.Gly70Glup.G70EP48380protein_codingdeleterious(0)probably_damaging(0.998)TCGA-AR-A1AX-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
RFX3SNVMissense_Mutationnovelc.160C>Tp.Pro54Serp.P54SP48380protein_codingtolerated(0.35)possibly_damaging(0.609)TCGA-AR-A251-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicinSD
RFX3SNVMissense_Mutationc.1129N>Ap.Glu377Lysp.E377KP48380protein_codingdeleterious(0)benign(0.041)TCGA-BH-A0W7-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxotereCR
RFX3SNVMissense_Mutationnovelc.581N>Gp.Ala194Glyp.A194GP48380protein_codingdeleterious(0.01)possibly_damaging(0.842)TCGA-D8-A13Y-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
RFX3SNVMissense_Mutationc.1042N>Ap.Glu348Lysp.E348KP48380protein_codingtolerated(0.13)benign(0.101)TCGA-D8-A27G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RFX3SNVMissense_Mutationc.1499C>Ap.Thr500Lysp.T500KP48380protein_codingdeleterious(0)probably_damaging(0.985)TCGA-E2-A159-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycyclophosphamideSD
RFX3insertionFrame_Shift_Insnovelc.135_136insTp.Val46CysfsTer50p.V46Cfs*50P48380protein_codingTCGA-A7-A13E-01Breastbreast invasive carcinomaFemale<65I/IITargeted Molecular therapybevacizumabPD
RFX3insertionFrame_Shift_Insnovelc.1747_1748insAAAGATTAAAAACAGCATTTATGACCTTTGTAGGTp.Pro583GlnfsTer29p.P583Qfs*29P48380protein_codingTCGA-A8-A06P-01Breastbreast invasive carcinomaFemale<65III/IVUnspecificSD
RFX3SNVMissense_Mutationrs777692576c.190N>Ap.Asp64Asnp.D64NP48380protein_codingdeleterious(0.05)benign(0.077)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
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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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