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: PLEKHA5

Gene summary for PLEKHA5

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PLEKHA5

Gene ID

54477

Gene namepleckstrin homology domain containing A5
Gene AliasPEPP-2
Cytomap12p12.3
Gene Typeprotein-coding
GO ID

GO:0007275

UniProtAcc

A0A024RAY7


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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
54477PLEKHA5CA_HPV_1HumanCervixCC6.88e-06-1.87e-010.0264
54477PLEKHA5CCI_1HumanCervixCC4.65e-061.09e+000.528
54477PLEKHA5CCI_2HumanCervixCC1.67e-081.44e+000.5249
54477PLEKHA5CCI_3HumanCervixCC3.56e-251.70e+000.516
54477PLEKHA5HTA11_3410_2000001011HumanColorectumAD7.86e-13-4.53e-010.0155
54477PLEKHA5HTA11_1938_2000001011HumanColorectumAD1.15e-034.74e-01-0.0811
54477PLEKHA5HTA11_347_2000001011HumanColorectumAD1.23e-116.34e-01-0.1954
54477PLEKHA5HTA11_3361_2000001011HumanColorectumAD1.27e-02-4.26e-01-0.1207
54477PLEKHA5HTA11_5216_2000001011HumanColorectumSER1.49e-02-6.51e-01-0.1462
54477PLEKHA5HTA11_9341_2000001011HumanColorectumSER1.99e-02-5.09e-01-0.00410000000000005
54477PLEKHA5HTA11_99999970781_79442HumanColorectumMSS1.10e-17-5.28e-010.294
54477PLEKHA5HTA11_99999965062_69753HumanColorectumMSI-H5.64e-117.82e-010.3487
54477PLEKHA5HTA11_99999973899_84307HumanColorectumMSS2.71e-05-6.57e-010.2585
54477PLEKHA5HTA11_99999974143_84620HumanColorectumMSS2.67e-09-4.66e-010.3005
54477PLEKHA5A015-C-203HumanColorectumFAP1.39e-30-5.77e-01-0.1294
54477PLEKHA5A015-C-204HumanColorectumFAP1.14e-05-3.48e-01-0.0228
54477PLEKHA5A014-C-040HumanColorectumFAP8.90e-03-3.09e-01-0.1184
54477PLEKHA5A002-C-201HumanColorectumFAP4.96e-12-3.73e-010.0324
54477PLEKHA5A001-C-119HumanColorectumFAP1.23e-05-2.43e-01-0.1557
54477PLEKHA5A001-C-108HumanColorectumFAP3.73e-09-1.76e-01-0.0272
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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
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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
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
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:00614588CervixCCreproductive system development87/2311427/187231.37e-064.55e-0587
GO:0061458ColorectumADreproductive system development116/3918427/187231.11e-031.01e-02116
GO:00614581ColorectumSERreproductive system development87/2897427/187233.69e-033.07e-0287
GO:00614582ColorectumMSSreproductive system development115/3467427/187239.86e-062.39e-04115
GO:00614583ColorectumFAPreproductive system development85/2622427/187234.30e-045.13e-0385
GO:00614584ColorectumCRCreproductive system development73/2078427/187231.13e-042.22e-0373
GO:00614589EndometriumAEHreproductive system development88/2100427/187239.50e-096.41e-0788
GO:006145815EndometriumEECreproductive system development91/2168427/187234.54e-093.13e-0791
GO:006145819EsophagusHGINreproductive system development78/2587427/187235.53e-034.52e-0278
GO:0061458110EsophagusESCCreproductive system development247/8552427/187232.24e-073.42e-06247
GO:00614585LiverCirrhoticreproductive system development132/4634427/187232.07e-031.28e-02132
GO:006145811LiverHCCreproductive system development205/7958427/187231.16e-024.27e-02205
GO:00614586LungIACreproductive system development79/2061427/187232.39e-061.06e-0479
GO:006145812LungAISreproductive system development70/1849427/187231.52e-055.50e-0470
GO:006145821LungAAHreproductive system development26/613427/187231.90e-034.35e-0226
GO:006145817Oral cavityOSCCreproductive system development217/7305427/187233.75e-075.63e-06217
GO:006145824Oral cavityEOLPreproductive system development81/2218427/187231.09e-051.93e-0481
GO:006145831Oral cavityNEOLPreproductive system development91/2005427/187238.18e-119.00e-0991
GO:006145810ProstateBPHreproductive system development126/3107427/187231.35e-119.95e-10126
GO:006145816ProstateTumorreproductive system development133/3246427/187231.24e-121.15e-10133
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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
PLEKHA5SNVMissense_Mutationrs760384877c.2983N>Cp.Glu995Glnp.E995QQ9HAU0protein_codingdeleterious(0.02)probably_damaging(0.989)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
PLEKHA5SNVMissense_Mutationc.3391N>Cp.Glu1131Glnp.E1131QQ9HAU0protein_codingtolerated(0.26)benign(0.048)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
PLEKHA5SNVMissense_Mutationnovelc.2050G>Ap.Glu684Lysp.E684KQ9HAU0protein_codingdeleterious(0.01)possibly_damaging(0.836)TCGA-AN-A0XW-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
PLEKHA5SNVMissense_Mutationrs376373462c.3685G>Ap.Glu1229Lysp.E1229KQ9HAU0protein_codingtolerated(0.12)benign(0.013)TCGA-AO-A128-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
PLEKHA5SNVMissense_Mutationc.2873G>Cp.Gly958Alap.G958AQ9HAU0protein_codingtolerated(0.23)benign(0.293)TCGA-BH-A18V-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PLEKHA5SNVMissense_Mutationc.2044G>Cp.Glu682Glnp.E682QQ9HAU0protein_codingdeleterious(0.04)probably_damaging(0.946)TCGA-E2-A10C-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PLEKHA5SNVMissense_Mutationc.2083N>Ap.Glu695Lysp.E695KQ9HAU0protein_codingtolerated(0.12)probably_damaging(0.985)TCGA-GM-A2D9-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
PLEKHA5insertionFrame_Shift_Insnovelc.3369_3370insCTAAp.Glu1124LeufsTer8p.E1124Lfs*8Q9HAU0protein_codingTCGA-A8-A09D-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinCR
PLEKHA5insertionNonsense_Mutationnovelc.3370_3371insTAAAATGTAAATp.Glu1124delinsValLysCysLysTerp.E1124delinsVKCK*Q9HAU0protein_codingTCGA-A8-A09D-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinCR
PLEKHA5insertionIn_Frame_Insnovelc.2423_2424insGACACGTACTAAGCAGTCCATp.Cys808delinsTrpThrArgThrLysGlnSerIlep.C808delinsWTRTKQSIQ9HAU0protein_codingTCGA-AN-A0FS-01Breastbreast invasive carcinomaFemale<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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