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: RUNX3

Gene summary for RUNX3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RUNX3

Gene ID

864

Gene nameRUNX family transcription factor 3
Gene AliasAML2
Cytomap1p36.11
Gene Typeprotein-coding
GO ID

GO:0000122

UniProtAcc

A0A024RAH4


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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
864RUNX3LZE24THumanEsophagusESCC4.97e-041.17e-010.0596
864RUNX3P2T-EHumanEsophagusESCC1.17e-275.38e-010.1177
864RUNX3P5T-EHumanEsophagusESCC6.89e-132.96e-010.1327
864RUNX3P8T-EHumanEsophagusESCC4.11e-042.65e-020.0889
864RUNX3P10T-EHumanEsophagusESCC8.70e-101.14e-010.116
864RUNX3P12T-EHumanEsophagusESCC2.20e-077.89e-020.1122
864RUNX3P15T-EHumanEsophagusESCC7.32e-061.83e-010.1149
864RUNX3P16T-EHumanEsophagusESCC1.14e-122.21e-010.1153
864RUNX3P20T-EHumanEsophagusESCC2.11e-043.94e-020.1124
864RUNX3P21T-EHumanEsophagusESCC2.78e-091.27e-010.1617
864RUNX3P27T-EHumanEsophagusESCC1.10e-081.78e-010.1055
864RUNX3P28T-EHumanEsophagusESCC8.87e-173.49e-010.1149
864RUNX3P30T-EHumanEsophagusESCC3.48e-021.54e-010.137
864RUNX3P31T-EHumanEsophagusESCC2.33e-071.93e-010.1251
864RUNX3P32T-EHumanEsophagusESCC1.78e-051.10e-010.1666
864RUNX3P37T-EHumanEsophagusESCC1.96e-058.93e-020.1371
864RUNX3P40T-EHumanEsophagusESCC7.38e-041.77e-010.109
864RUNX3P48T-EHumanEsophagusESCC6.12e-071.06e-010.0959
864RUNX3P52T-EHumanEsophagusESCC2.20e-059.49e-020.1555
864RUNX3P56T-EHumanEsophagusESCC6.04e-095.96e-010.1613
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
∗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:00457865EsophagusESCCnegative regulation of cell cycle236/8552385/187233.62e-109.93e-09236
GO:004578527EsophagusESCCpositive regulation of cell adhesion255/8552437/187235.07e-089.11e-07255
GO:00715599EsophagusESCCresponse to transforming growth factor beta157/8552256/187232.95e-074.23e-06157
GO:000150317EsophagusESCCossification232/8552408/187233.00e-063.40e-05232
GO:005067318EsophagusESCCepithelial cell proliferation238/8552437/187231.19e-048.20e-04238
GO:1903706110EsophagusESCCregulation of hemopoiesis201/8552367/187232.60e-041.58e-03201
GO:19021076EsophagusESCCpositive regulation of leukocyte differentiation93/8552157/187234.20e-042.39e-0393
GO:19037086EsophagusESCCpositive regulation of hemopoiesis93/8552157/187234.20e-042.39e-0393
GO:005067817EsophagusESCCregulation of epithelial cell proliferation206/8552381/187235.51e-043.02e-03206
GO:002240720EsophagusESCCregulation of cell-cell adhesion239/8552448/187235.88e-043.19e-03239
GO:000268316EsophagusESCCnegative regulation of immune system process231/8552434/187238.48e-044.36e-03231
GO:004211018EsophagusESCCT cell activation256/8552487/187231.18e-035.87e-03256
GO:19031317EsophagusESCCmononuclear cell differentiation226/8552426/187231.20e-035.88e-03226
GO:002240919EsophagusESCCpositive regulation of cell-cell adhesion155/8552284/187231.50e-037.06e-03155
GO:190210510EsophagusESCCregulation of leukocyte differentiation152/8552279/187231.82e-038.35e-03152
GO:00456213EsophagusESCCpositive regulation of lymphocyte differentiation61/8552104/187235.22e-031.97e-0261
GO:005087015EsophagusESCCpositive regulation of T cell activation117/8552216/187237.23e-032.62e-02117
GO:00302176EsophagusESCCT cell differentiation137/8552257/187238.09e-032.87e-02137
GO:190303916EsophagusESCCpositive regulation of leukocyte cell-cell adhesion128/8552239/187238.40e-032.96e-02128
GO:000715918EsophagusESCCleukocyte cell-cell adhesion192/8552371/187231.03e-023.51e-02192
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05169210EsophagusESCCEpstein-Barr virus infection151/4205202/84651.55e-133.45e-121.77e-12151
hsa046585EsophagusESCCTh1 and Th2 cell differentiation58/420592/84656.49e-031.60e-028.19e-0358
hsa0516937EsophagusESCCEpstein-Barr virus infection151/4205202/84651.55e-133.45e-121.77e-12151
hsa0465812EsophagusESCCTh1 and Th2 cell differentiation58/420592/84656.49e-031.60e-028.19e-0358
hsa0516928Oral cavityOSCCEpstein-Barr virus infection144/3704202/84651.08e-153.60e-141.83e-14144
hsa046584Oral cavityOSCCTh1 and Th2 cell differentiation53/370492/84655.00e-031.20e-026.13e-0353
hsa05169113Oral cavityOSCCEpstein-Barr virus infection144/3704202/84651.08e-153.60e-141.83e-14144
hsa0465811Oral cavityOSCCTh1 and Th2 cell differentiation53/370492/84655.00e-031.20e-026.13e-0353
hsa0516943Oral cavityEOLPEpstein-Barr virus infection66/1218202/84652.23e-111.20e-097.08e-1066
hsa0465821Oral cavityEOLPTh1 and Th2 cell differentiation31/121892/84652.27e-061.79e-051.05e-0531
hsa0516953Oral cavityEOLPEpstein-Barr virus infection66/1218202/84652.23e-111.20e-097.08e-1066
hsa0465831Oral cavityEOLPTh1 and Th2 cell differentiation31/121892/84652.27e-061.79e-051.05e-0531
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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
RUNX3LUMPBreastIDCCORO1A,SPRR2A,CSTB, etc.2.84e-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.
RUNX3CD8TCMBreastADJCCL5,NKG7,GNLY, etc.4.79e-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.
RUNX3CD8TEXINTBreastDCISCCL5,NKG7,GNLY, etc.1.60e-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.
RUNX3CD8TEREXBreastDCISCCL5,NKG7,GNLY, etc.1.71e-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.
RUNX3CD8TCMBreastDCISCCL5,NKG7,GNLY, etc.9.24e-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.
RUNX3CD8TRMBreastHealthyCCL5,NKG7,GNLY, etc.3.94e-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.
RUNX3CD8TEREXBreastHealthyCCL5,NKG7,GNLY, etc.9.00e-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.
RUNX3CD8TCMBreastIDCCCL5,NKG7,GNLY, etc.2.70e-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.
RUNX3CD8TEREXBreastIDCCCL5,NKG7,GNLY, etc.8.37e-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.
RUNX3CD8TCMBreastPrecancerCCL5,NKG7,GNLY, etc.5.81e-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
RUNX3SNVMissense_Mutationc.968C>Tp.Pro323Leup.P323LQ13761protein_codingdeleterious(0)probably_damaging(0.998)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
RUNX3SNVMissense_Mutationnovelc.406C>Tp.Arg136Cysp.R136CQ13761protein_codingdeleterious(0)probably_damaging(0.998)TCGA-EA-A3HU-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
RUNX3SNVMissense_Mutationrs759577669c.457N>Tp.Arg153Cysp.R153CQ13761protein_codingdeleterious(0.03)probably_damaging(0.999)TCGA-EK-A3GM-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
RUNX3SNVMissense_Mutationrs764020894c.935N>Tp.Pro312Leup.P312LQ13761protein_codingdeleterious(0.04)possibly_damaging(0.46)TCGA-FU-A3YQ-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
RUNX3SNVMissense_Mutationrs753532923c.341A>Gp.Asp114Glyp.D114GQ13761protein_codingdeleterious(0)benign(0.178)TCGA-A6-5665-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
RUNX3SNVMissense_Mutationc.655N>Tp.Arg219Cysp.R219CQ13761protein_codingdeleterious(0)possibly_damaging(0.649)TCGA-AA-3947-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
RUNX3SNVMissense_Mutationnovelc.697N>Tp.Leu233Phep.L233FQ13761protein_codingdeleterious(0.02)benign(0.084)TCGA-AA-3950-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
RUNX3SNVMissense_Mutationrs752706729c.1105C>Tp.Arg369Cysp.R369CQ13761protein_codingdeleterious(0)probably_damaging(0.998)TCGA-AD-6964-01Colorectumcolon adenocarcinomaMale<65III/IVChemotherapyfolfoxPD
RUNX3SNVMissense_Mutationrs193187661c.8N>Tp.Ser3Leup.S3LQ13761protein_codingdeleterious_low_confidence(0)probably_damaging(0.921)TCGA-CA-6717-01Colorectumcolon adenocarcinomaMale<65I/IIChemotherapyoxaliplatinCR
RUNX3SNVMissense_Mutationc.655N>Tp.Arg219Cysp.R219CQ13761protein_codingdeleterious(0)possibly_damaging(0.649)TCGA-G4-6628-01Colorectumcolon adenocarcinomaMale>=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
864RUNX3TRANSCRIPTION FACTORLEUCOVORINLEUCOVORIN17372756
864RUNX3TRANSCRIPTION FACTORIRINOTECANIRINOTECAN17372756
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