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: EYA3

Gene summary for EYA3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

EYA3

Gene ID

2140

Gene nameEYA transcriptional coactivator and phosphatase 3
Gene AliasEYA3
Cytomap1p35.3
Gene Typeprotein-coding
GO ID

GO:0003008

UniProtAcc

Q99504


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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
2140EYA3CCI_1HumanCervixCC4.62e-055.95e-010.528
2140EYA3CCI_2HumanCervixCC4.77e-067.15e-010.5249
2140EYA3CCI_3HumanCervixCC1.97e-106.25e-010.516
2140EYA3HTA11_99999974143_84620HumanColorectumMSS1.43e-04-3.57e-010.3005
2140EYA3F007HumanColorectumFAP4.08e-02-2.85e-010.1176
2140EYA3A001-C-207HumanColorectumFAP2.64e-04-3.13e-010.1278
2140EYA3A015-C-203HumanColorectumFAP1.34e-24-4.19e-01-0.1294
2140EYA3A015-C-204HumanColorectumFAP1.41e-05-2.68e-01-0.0228
2140EYA3A014-C-040HumanColorectumFAP1.90e-04-4.25e-01-0.1184
2140EYA3A002-C-201HumanColorectumFAP3.68e-15-3.97e-010.0324
2140EYA3A002-C-203HumanColorectumFAP4.07e-04-2.76e-010.2786
2140EYA3A001-C-119HumanColorectumFAP1.93e-05-3.33e-01-0.1557
2140EYA3A001-C-108HumanColorectumFAP1.44e-17-4.27e-01-0.0272
2140EYA3A002-C-205HumanColorectumFAP2.56e-23-5.11e-01-0.1236
2140EYA3A001-C-104HumanColorectumFAP2.42e-03-2.45e-010.0184
2140EYA3A015-C-005HumanColorectumFAP3.87e-07-3.19e-01-0.0336
2140EYA3A015-C-006HumanColorectumFAP5.85e-17-4.94e-01-0.0994
2140EYA3A015-C-106HumanColorectumFAP2.59e-11-3.96e-01-0.0511
2140EYA3A002-C-114HumanColorectumFAP1.25e-18-4.66e-01-0.1561
2140EYA3A015-C-104HumanColorectumFAP2.82e-26-5.10e-01-0.1899
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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
∗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:200123310CervixCCregulation of apoptotic signaling pathway96/2311356/187234.08e-143.05e-1196
GO:200123410CervixCCnegative regulation of apoptotic signaling pathway56/2311224/187231.39e-076.70e-0656
GO:009719110CervixCCextrinsic apoptotic signaling pathway52/2311219/187232.06e-066.34e-0552
GO:00064708CervixCCprotein dephosphorylation60/2311281/187231.33e-052.68e-0460
GO:200123610CervixCCregulation of extrinsic apoptotic signaling pathway37/2311151/187232.80e-054.65e-0437
GO:00093149CervixCCresponse to radiation86/2311456/187233.50e-055.63e-0486
GO:00165705CervixCChistone modification84/2311463/187231.70e-042.01e-0384
GO:20010209CervixCCregulation of response to DNA damage stimulus46/2311219/187231.92e-042.23e-0346
GO:00102126CervixCCresponse to ionizing radiation34/2311148/187232.23e-042.53e-0334
GO:00510528CervixCCregulation of DNA metabolic process65/2311359/187239.25e-047.84e-0365
GO:00163117CervixCCdephosphorylation73/2311417/187231.23e-039.87e-0373
GO:200123710CervixCCnegative regulation of extrinsic apoptotic signaling pathway23/231197/187231.39e-031.10e-0223
GO:20012332ColorectumMSSregulation of apoptotic signaling pathway116/3467356/187231.02e-101.06e-08116
GO:00510522ColorectumMSSregulation of DNA metabolic process108/3467359/187235.86e-083.10e-06108
GO:00510542ColorectumMSSpositive regulation of DNA metabolic process69/3467201/187236.33e-083.26e-0669
GO:20012342ColorectumMSSnegative regulation of apoptotic signaling pathway72/3467224/187236.17e-072.29e-0572
GO:20010202ColorectumMSSregulation of response to DNA damage stimulus64/3467219/187237.20e-051.21e-0364
GO:00971912ColorectumMSSextrinsic apoptotic signaling pathway63/3467219/187231.34e-042.03e-0363
GO:0016570ColorectumMSShistone modification113/3467463/187238.37e-048.68e-03113
GO:20010221ColorectumMSSpositive regulation of response to DNA damage stimulus33/3467105/187239.83e-049.86e-0333
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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
∗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
EYA3SNVMissense_Mutationnovelc.1676N>Ap.Gly559Glup.G559EQ99504protein_codingdeleterious(0.02)possibly_damaging(0.463)TCGA-AN-A04C-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
EYA3SNVMissense_Mutationc.607N>Gp.Leu203Valp.L203VQ99504protein_codingtolerated(0.05)benign(0.355)TCGA-B6-A0IJ-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
EYA3SNVMissense_Mutationc.1551N>Gp.Ser517Argp.S517RQ99504protein_codingdeleterious(0)probably_damaging(0.998)TCGA-E9-A22H-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
EYA3insertionFrame_Shift_Insnovelc.1324_1325insTGCAGTACACTAATGCTATGAAGCCCp.Lys442MetfsTer16p.K442Mfs*16Q99504protein_codingTCGA-A8-A07J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapy5-fluorouracilCR
EYA3insertionNonsense_Mutationnovelc.1468_1469insGAGACTCCGTCTCTAAATAAATAAATAAAAGGTATTGACAAGGAp.Leu490ArgfsTer7p.L490Rfs*7Q99504protein_codingTCGA-AN-A0FW-01Breastbreast invasive carcinomaFemale>=65III/IVUnknownUnknownSD
EYA3insertionFrame_Shift_Insnovelc.634_635insCTTTCTATGTCCAGGATCCCTTTAAGATTCTGAGGAAAGCATGGp.Tyr212SerfsTer36p.Y212Sfs*36Q99504protein_codingTCGA-BH-A0HX-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadrimycinSD
EYA3SNVMissense_Mutationc.292A>Cp.Thr98Prop.T98PQ99504protein_codingtolerated(0.14)benign(0.006)TCGA-FU-A3HZ-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
EYA3SNVMissense_Mutationnovelc.1253N>Ap.Arg418Hisp.R418HQ99504protein_codingdeleterious(0)probably_damaging(1)TCGA-ZJ-AAXN-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
EYA3SNVMissense_Mutationc.1505T>Cp.Phe502Serp.F502SQ99504protein_codingdeleterious(0)probably_damaging(0.999)TCGA-A6-5665-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
EYA3SNVMissense_Mutationc.781N>Cp.Thr261Prop.T261PQ99504protein_codingtolerated(0.1)benign(0)TCGA-G4-6586-01Colorectumcolon adenocarcinomaFemale>=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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