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: PREP

Gene summary for PREP

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PREP

Gene ID

5550

Gene nameprolyl endopeptidase
Gene AliasPE
Cytomap6q21
Gene Typeprotein-coding
GO ID

GO:0006508

UniProtAcc

B2RAH7


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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
5550PREPHTA11_3410_2000001011HumanColorectumAD1.15e-06-4.95e-010.0155
5550PREPHTA11_3361_2000001011HumanColorectumAD1.25e-11-7.09e-01-0.1207
5550PREPHTA11_696_2000001011HumanColorectumAD5.51e-08-4.14e-01-0.1464
5550PREPHTA11_99999965104_69814HumanColorectumMSS1.72e-034.59e-010.281
5550PREPHTA11_99999973899_84307HumanColorectumMSS6.93e-03-5.67e-010.2585
5550PREPHTA11_99999974143_84620HumanColorectumMSS4.87e-28-7.13e-010.3005
5550PREPA002-C-010HumanColorectumFAP1.12e-02-1.65e-010.242
5550PREPA001-C-207HumanColorectumFAP1.72e-03-4.01e-010.1278
5550PREPA015-C-203HumanColorectumFAP3.64e-43-5.88e-01-0.1294
5550PREPA015-C-204HumanColorectumFAP1.79e-06-3.81e-01-0.0228
5550PREPA014-C-040HumanColorectumFAP1.28e-04-5.19e-01-0.1184
5550PREPA002-C-201HumanColorectumFAP6.86e-17-4.76e-010.0324
5550PREPA002-C-203HumanColorectumFAP8.49e-06-1.66e-010.2786
5550PREPA001-C-119HumanColorectumFAP8.78e-10-5.45e-01-0.1557
5550PREPA001-C-108HumanColorectumFAP2.77e-24-3.59e-01-0.0272
5550PREPA002-C-205HumanColorectumFAP9.83e-28-5.10e-01-0.1236
5550PREPA001-C-104HumanColorectumFAP1.71e-07-1.80e-010.0184
5550PREPA015-C-005HumanColorectumFAP3.10e-03-9.10e-02-0.0336
5550PREPA015-C-006HumanColorectumFAP2.28e-20-6.11e-01-0.0994
5550PREPA015-C-106HumanColorectumFAP1.35e-18-3.86e-01-0.0511
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
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
∗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:004819318EsophagusESCCGolgi vesicle transport231/8552296/187231.82e-309.63e-28231
GO:001619715EsophagusESCCendosomal transport168/8552230/187232.28e-171.93e-15168
GO:0090150110EsophagusESCCestablishment of protein localization to membrane182/8552260/187231.27e-158.19e-14182
GO:0072659110EsophagusESCCprotein localization to plasma membrane193/8552284/187231.95e-141.03e-12193
GO:001648210EsophagusESCCcytosolic transport124/8552168/187239.69e-144.69e-12124
GO:199077819EsophagusESCCprotein localization to cell periphery217/8552333/187234.08e-131.88e-11217
GO:000689215EsophagusESCCpost-Golgi vesicle-mediated transport82/8552104/187234.00e-121.55e-1082
GO:009887615EsophagusESCCvesicle-mediated transport to the plasma membrane99/8552136/187231.13e-103.39e-0999
GO:000689315EsophagusESCCGolgi to plasma membrane transport48/855260/187235.11e-089.16e-0748
GO:004300114EsophagusESCCGolgi to plasma membrane protein transport34/855240/187233.00e-074.27e-0634
GO:00421477EsophagusESCCretrograde transport, endosome to Golgi63/855291/187234.58e-064.87e-0563
GO:006195114EsophagusESCCestablishment of protein localization to plasma membrane44/855260/187231.25e-051.15e-0444
GO:004819311LiverCirrhoticGolgi vesicle transport153/4634296/187231.02e-236.43e-21153
GO:00901507LiverCirrhoticestablishment of protein localization to membrane123/4634260/187231.85e-152.15e-13123
GO:199077811LiverCirrhoticprotein localization to cell periphery135/4634333/187231.18e-106.21e-09135
GO:007265911LiverCirrhoticprotein localization to plasma membrane119/4634284/187231.30e-106.80e-09119
GO:004300111LiverCirrhoticGolgi to plasma membrane protein transport27/463440/187231.43e-085.36e-0727
GO:001648211LiverCirrhoticcytosolic transport74/4634168/187233.34e-081.12e-0674
GO:000689211LiverCirrhoticpost-Golgi vesicle-mediated transport51/4634104/187237.12e-082.15e-0651
GO:001619711LiverCirrhoticendosomal transport93/4634230/187231.01e-072.93e-0693
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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
PREPSNVMissense_Mutationnovelc.1915N>Ap.Asp639Asnp.D639NP48147protein_codingdeleterious(0)probably_damaging(0.976)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
PREPSNVMissense_Mutationnovelc.130N>Ap.Glu44Lysp.E44KP48147protein_codingtolerated(0.21)benign(0.021)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
PREPSNVMissense_Mutationc.1956N>Gp.Phe652Leup.F652LP48147protein_codingtolerated(0.87)benign(0.02)TCGA-A8-A06Q-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
PREPSNVMissense_Mutationc.1582G>Ap.Asp528Asnp.D528NP48147protein_codingtolerated(0.08)benign(0.434)TCGA-A8-A092-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapypaclitaxelCR
PREPSNVMissense_Mutationc.62N>Tp.Gly21Valp.G21VP48147protein_codingdeleterious(0)probably_damaging(0.998)TCGA-A8-A09C-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PREPSNVMissense_Mutationnovelc.58N>Tp.His20Tyrp.H20YP48147protein_codingdeleterious(0.02)possibly_damaging(0.6)TCGA-AN-A0XW-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
PREPSNVMissense_Mutationc.1301N>Gp.Asp434Glyp.D434GP48147protein_codingtolerated(0.29)benign(0.013)TCGA-BH-A18G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PREPSNVMissense_Mutationc.715G>Ap.Glu239Lysp.E239KP48147protein_codingtolerated(0.25)benign(0.081)TCGA-C8-A1HF-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PREPSNVMissense_Mutationc.34G>Cp.Asp12Hisp.D12HP48147protein_codingdeleterious(0)probably_damaging(0.937)TCGA-D8-A1JA-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinPD
PREPinsertionIn_Frame_Insnovelc.285_286insCTTAGAATAATAAACATTTGTTTTTGCTATGAGCCTp.Gln95_Asn96insLeuArgIleIleAsnIleCysPheCysTyrGluProp.Q95_N96insLRIINICFCYEPP48147protein_codingTCGA-A8-A097-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
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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
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMEinhibitor405560408
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMEONO-1603CHEMBL1087333
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMESTZSTREPTOZOCIN8190911
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMES-17092-1
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMEinhibitor252166765
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMEALV-003LATIGLUTENASE
5550PREPPROTEASE, ENZYME, DRUGGABLE GENOMEinhibitor178103179
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