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: PSENEN

Gene summary for PSENEN

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PSENEN

Gene ID

55851

Gene namepresenilin enhancer, gamma-secretase subunit
Gene AliasACNINV2
Cytomap19q13.12
Gene Typeprotein-coding
GO ID

GO:0006508

UniProtAcc

Q9NZ42


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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
55851PSENENHTA11_10623_2000001011HumanColorectumAD8.98e-031.87e-01-0.0177
55851PSENENHTA11_10711_2000001011HumanColorectumAD4.64e-041.74e-010.0338
55851PSENENHTA11_7696_3000711011HumanColorectumAD1.58e-132.58e-010.0674
55851PSENENHTA11_6818_2000001011HumanColorectumAD9.33e-072.74e-010.0112
55851PSENENHTA11_6818_2000001021HumanColorectumAD3.40e-072.88e-010.0588
55851PSENENHTA11_99999970781_79442HumanColorectumMSS4.28e-102.48e-010.294
55851PSENENHTA11_99999965062_69753HumanColorectumMSI-H5.36e-075.36e-010.3487
55851PSENENHTA11_99999965104_69814HumanColorectumMSS4.35e-154.56e-010.281
55851PSENENHTA11_99999971662_82457HumanColorectumMSS1.23e-234.79e-010.3859
55851PSENENHTA11_99999973899_84307HumanColorectumMSS8.26e-072.82e-010.2585
55851PSENENHTA11_99999974143_84620HumanColorectumMSS4.47e-082.02e-010.3005
55851PSENENLZE2THumanEsophagusESCC1.10e-038.90e-010.082
55851PSENENLZE4THumanEsophagusESCC1.61e-154.06e-010.0811
55851PSENENLZE5THumanEsophagusESCC6.07e-065.27e-010.0514
55851PSENENLZE7THumanEsophagusESCC5.29e-055.77e-010.0667
55851PSENENLZE8THumanEsophagusESCC9.45e-102.61e-010.067
55851PSENENLZE20THumanEsophagusESCC3.46e-073.84e-010.0662
55851PSENENLZE22D1HumanEsophagusHGIN1.14e-041.17e-010.0595
55851PSENENLZE22THumanEsophagusESCC8.07e-086.08e-010.068
55851PSENENLZE24THumanEsophagusESCC2.78e-271.28e+000.0596
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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
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:0045862ColorectumADpositive regulation of proteolysis129/3918372/187234.04e-103.46e-08129
GO:0052547ColorectumADregulation of peptidase activity137/3918461/187234.12e-061.12e-04137
GO:0010952ColorectumADpositive regulation of peptidase activity68/3918197/187236.30e-061.59e-0468
GO:0052548ColorectumADregulation of endopeptidase activity124/3918432/187236.58e-051.07e-03124
GO:0010950ColorectumADpositive regulation of endopeptidase activity59/3918179/187231.11e-041.65e-0359
GO:0051604ColorectumADprotein maturation85/3918294/187236.73e-046.91e-0385
GO:0033619ColorectumADmembrane protein proteolysis21/391857/187234.16e-032.88e-0221
GO:0016485ColorectumADprotein processing63/3918225/187236.77e-034.19e-0263
GO:0007219ColorectumADNotch signaling pathway50/3918172/187236.92e-034.26e-0250
GO:00458621ColorectumSERpositive regulation of proteolysis106/2897372/187238.40e-111.20e-08106
GO:00525471ColorectumSERregulation of peptidase activity114/2897461/187231.18e-077.17e-06114
GO:00525481ColorectumSERregulation of endopeptidase activity103/2897432/187232.86e-061.16e-04103
GO:00109521ColorectumSERpositive regulation of peptidase activity55/2897197/187235.44e-062.00e-0455
GO:00516041ColorectumSERprotein maturation73/2897294/187231.82e-055.38e-0473
GO:00109501ColorectumSERpositive regulation of endopeptidase activity47/2897179/187231.32e-042.66e-0347
GO:00164851ColorectumSERprotein processing55/2897225/187232.84e-044.67e-0355
GO:00458622ColorectumMSSpositive regulation of proteolysis119/3467372/187232.14e-102.09e-08119
GO:00525472ColorectumMSSregulation of peptidase activity130/3467461/187231.81e-078.13e-06130
GO:00109522ColorectumMSSpositive regulation of peptidase activity63/3467197/187233.65e-061.06e-0463
GO:00525482ColorectumMSSregulation of endopeptidase activity117/3467432/187236.25e-061.65e-04117
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05010ColorectumADAlzheimer disease174/2092384/84651.82e-199.26e-185.91e-18174
hsa050101ColorectumADAlzheimer disease174/2092384/84651.82e-199.26e-185.91e-18174
hsa050102ColorectumSERAlzheimer disease146/1580384/84656.52e-202.40e-181.75e-18146
hsa050103ColorectumSERAlzheimer disease146/1580384/84656.52e-202.40e-181.75e-18146
hsa050104ColorectumMSSAlzheimer disease169/1875384/84651.21e-221.01e-206.21e-21169
hsa050105ColorectumMSSAlzheimer disease169/1875384/84651.21e-221.01e-206.21e-21169
hsa050106ColorectumMSI-HAlzheimer disease91/797384/84651.76e-176.41e-165.37e-1691
hsa050107ColorectumMSI-HAlzheimer disease91/797384/84651.76e-176.41e-165.37e-1691
hsa0501030EsophagusHGINAlzheimer disease130/1383384/84655.26e-181.71e-161.36e-16130
hsa05010113EsophagusHGINAlzheimer disease130/1383384/84655.26e-181.71e-161.36e-16130
hsa05010210EsophagusESCCAlzheimer disease263/4205384/84651.80e-145.47e-132.80e-13263
hsa043306EsophagusESCCNotch signaling pathway42/420562/84652.97e-037.97e-034.08e-0342
hsa0501038EsophagusESCCAlzheimer disease263/4205384/84651.80e-145.47e-132.80e-13263
hsa0433013EsophagusESCCNotch signaling pathway42/420562/84652.97e-037.97e-034.08e-0342
hsa0501014LiverCirrhoticAlzheimer disease180/2530384/84655.52e-131.36e-118.36e-12180
hsa0501015LiverCirrhoticAlzheimer disease180/2530384/84655.52e-131.36e-118.36e-12180
hsa0501022LiverHCCAlzheimer disease254/4020384/84653.75e-148.97e-134.99e-13254
hsa0501032LiverHCCAlzheimer disease254/4020384/84653.75e-148.97e-134.99e-13254
hsa0501028Oral cavityOSCCAlzheimer disease244/3704384/84651.18e-153.60e-141.83e-14244
hsa043305Oral cavityOSCCNotch signaling pathway44/370462/84651.26e-055.55e-052.83e-0544
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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
PSENENSNVMissense_Mutationrs758352978c.116N>Ap.Arg39Glnp.R39QQ9NZ42protein_codingtolerated(0.16)benign(0.009)TCGA-E2-A1LH-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
PSENENSNVMissense_Mutationnovelc.176N>Ap.Arg59Hisp.R59HQ9NZ42protein_codingtolerated(0.54)possibly_damaging(0.616)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
PSENENSNVMissense_Mutationnovelc.121N>Cp.Ala41Prop.A41PQ9NZ42protein_codingdeleterious(0)probably_damaging(0.999)TCGA-A5-A1OF-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
PSENENSNVMissense_Mutationrs201796315c.127N>Tp.Leu43Phep.L43FQ9NZ42protein_codingtolerated(0.7)benign(0.007)TCGA-AX-A2HD-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnknownUnknownSD
PSENENSNVMissense_Mutationnovelc.19N>Cp.Ser7Prop.S7PQ9NZ42protein_codingtolerated(1)benign(0.007)TCGA-EO-A22R-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
PSENENSNVMissense_Mutationc.127C>Gp.Leu43Valp.L43VQ9NZ42protein_codingtolerated(0.5)benign(0.007)TCGA-93-7347-01Lunglung adenocarcinomaFemale>=65I/IIUnknownUnknownSD
PSENENSNVMissense_Mutationc.90G>Tp.Trp30Cysp.W30CQ9NZ42protein_codingdeleterious(0)probably_damaging(0.998)TCGA-70-6722-01Lunglung squamous cell carcinomaMale<65III/IVUnknownUnknownPD
PSENENSNVMissense_Mutationnovelc.236A>Gp.Gln79Argp.Q79RQ9NZ42protein_codingdeleterious(0.01)probably_damaging(0.982)TCGA-77-7141-01Lunglung squamous cell carcinomaMale<65I/IIUnknownUnknownSD
PSENENSNVMissense_Mutationnovelc.61G>Cp.Gly21Argp.G21RQ9NZ42protein_codingdeleterious(0.02)probably_damaging(1)TCGA-77-7465-01Lunglung squamous cell carcinomaMale<65I/IIUnknownUnknownSD
PSENENSNVMissense_Mutationnovelc.25N>Ap.Glu9Lysp.E9KQ9NZ42protein_codingdeleterious(0.03)possibly_damaging(0.509)TCGA-85-A4CL-01Lunglung squamous cell carcinomaMale>=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
55851PSENENDRUGGABLE GENOMEinhibitorRO 4929097
55851PSENENDRUGGABLE GENOMEinhibitorCHEMBL1090771AVAGACESTAT
55851PSENENDRUGGABLE GENOMEBMS-299897CHEMBL247471
55851PSENENDRUGGABLE GENOMELY-411575CHEMBL39206823181502,19443228
55851PSENENDRUGGABLE GENOMEinhibitorPF03084014
55851PSENENDRUGGABLE GENOMEinhibitorMK0752
55851PSENENDRUGGABLE GENOMENIC5-15METHYLINOSITOL
55851PSENENDRUGGABLE GENOMEGSI-136GSI-136
55851PSENENDRUGGABLE GENOMESEMAGACESTATSEMAGACESTAT19443228
55851PSENENDRUGGABLE GENOMEinhibitorCHEMBL463981BEGACESTAT
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