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: VPS4A

Gene summary for VPS4A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

VPS4A

Gene ID

27183

Gene namevacuolar protein sorting 4 homolog A
Gene AliasCIMDAG
Cytomap16q22.1
Gene Typeprotein-coding
GO ID

GO:0000070

UniProtAcc

A0A024R705


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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
27183VPS4AHTA11_2487_2000001011HumanColorectumSER1.12e-032.67e-01-0.1808
27183VPS4AHTA11_1938_2000001011HumanColorectumAD4.54e-022.41e-01-0.0811
27183VPS4AHTA11_347_2000001011HumanColorectumAD4.36e-092.67e-01-0.1954
27183VPS4AHTA11_411_2000001011HumanColorectumSER3.82e-034.16e-01-0.2602
27183VPS4AHTA11_83_2000001011HumanColorectumSER4.58e-032.58e-01-0.1526
27183VPS4AHTA11_696_2000001011HumanColorectumAD3.80e-092.83e-01-0.1464
27183VPS4AHTA11_866_2000001011HumanColorectumAD2.73e-031.43e-01-0.1001
27183VPS4AHTA11_1391_2000001011HumanColorectumAD6.00e-062.82e-01-0.059
27183VPS4AHTA11_2992_2000001011HumanColorectumSER5.34e-034.37e-01-0.1706
27183VPS4AHTA11_7696_3000711011HumanColorectumAD3.33e-041.97e-010.0674
27183VPS4AHTA11_99999970781_79442HumanColorectumMSS2.53e-021.71e-010.294
27183VPS4AHTA11_99999971662_82457HumanColorectumMSS3.05e-185.40e-010.3859
27183VPS4AHTA11_99999974143_84620HumanColorectumMSS7.27e-042.55e-010.3005
27183VPS4ALZE4THumanEsophagusESCC2.21e-102.46e-010.0811
27183VPS4ALZE7THumanEsophagusESCC8.08e-041.23e-010.0667
27183VPS4ALZE8THumanEsophagusESCC3.82e-02-3.35e-020.067
27183VPS4ALZE20THumanEsophagusESCC1.72e-032.75e-010.0662
27183VPS4ALZE22D1HumanEsophagusHGIN2.01e-041.48e-010.0595
27183VPS4ALZE22THumanEsophagusESCC2.37e-076.93e-010.068
27183VPS4ALZE24THumanEsophagusESCC7.00e-225.55e-010.0596
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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
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:19019908ThyroidPTCregulation of mitotic cell cycle phase transition138/5968299/187231.44e-072.78e-06138
GO:000704115ThyroidPTClysosomal transport63/5968114/187231.97e-073.54e-0663
GO:1903076112ThyroidPTCregulation of protein localization to plasma membrane58/5968104/187233.91e-076.51e-0658
GO:000703210ThyroidPTCendosome organization48/596882/187235.65e-079.04e-0648
GO:00002818ThyroidPTCmitotic cytokinesis43/596871/187235.93e-079.47e-0643
GO:0030865110ThyroidPTCcortical cytoskeleton organization38/596861/187239.77e-071.46e-0538
GO:199018215ThyroidPTCexosomal secretion17/596820/187231.39e-061.98e-0517
GO:00457867ThyroidPTCnegative regulation of cell cycle166/5968385/187231.93e-062.64e-05166
GO:19019878ThyroidPTCregulation of cell cycle phase transition167/5968390/187232.97e-063.87e-05167
GO:00482846ThyroidPTCorganelle fusion71/5968141/187233.68e-064.70e-0571
GO:004409110ThyroidPTCmembrane biogenesis34/596855/187234.64e-065.69e-0534
GO:009773415ThyroidPTCextracellular exosome biogenesis17/596821/187235.13e-066.22e-0517
GO:014011210ThyroidPTCextracellular vesicle biogenesis18/596823/187236.38e-067.63e-0518
GO:001906816ThyroidPTCvirion assembly24/596835/187239.08e-061.03e-0424
GO:007170914ThyroidPTCmembrane assembly31/596850/187231.12e-051.23e-0431
GO:0031032110ThyroidPTCactomyosin structure organization91/5968196/187231.35e-051.45e-0491
GO:000091019ThyroidPTCcytokinesis82/5968173/187231.37e-051.47e-0482
GO:1903900113ThyroidPTCregulation of viral life cycle72/5968148/187231.49e-051.58e-0472
GO:19035439ThyroidPTCpositive regulation of exosomal secretion13/596815/187231.81e-051.87e-0413
GO:007266518ThyroidPTCprotein localization to vacuole38/596867/187232.28e-052.28e-0438
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa04144ColorectumADEndocytosis111/2092251/84655.95e-121.42e-109.08e-11111
hsa041441ColorectumADEndocytosis111/2092251/84655.95e-121.42e-109.08e-11111
hsa041442ColorectumSEREndocytosis81/1580251/84651.14e-072.36e-061.71e-0681
hsa04217ColorectumSERNecroptosis47/1580159/84655.21e-044.44e-033.22e-0347
hsa041443ColorectumSEREndocytosis81/1580251/84651.14e-072.36e-061.71e-0681
hsa042171ColorectumSERNecroptosis47/1580159/84655.21e-044.44e-033.22e-0347
hsa041444ColorectumMSSEndocytosis102/1875251/84651.85e-114.43e-102.71e-10102
hsa03250ColorectumMSSViral life cycle - HIV-123/187563/84656.55e-032.64e-021.62e-0223
hsa041445ColorectumMSSEndocytosis102/1875251/84651.85e-114.43e-102.71e-10102
hsa032501ColorectumMSSViral life cycle - HIV-123/187563/84656.55e-032.64e-021.62e-0223
hsa0414429EsophagusHGINEndocytosis76/1383251/84651.74e-083.34e-072.65e-0776
hsa04144113EsophagusHGINEndocytosis76/1383251/84651.74e-083.34e-072.65e-0776
hsa04144210EsophagusESCCEndocytosis186/4205251/84659.74e-164.66e-142.39e-14186
hsa032509EsophagusESCCViral life cycle - HIV-154/420563/84652.01e-092.17e-081.11e-0854
hsa0414437EsophagusESCCEndocytosis186/4205251/84659.74e-164.66e-142.39e-14186
hsa0325014EsophagusESCCViral life cycle - HIV-154/420563/84652.01e-092.17e-081.11e-0854
hsa0414422LiverHCCEndocytosis178/4020251/84652.03e-145.22e-132.91e-13178
hsa032502LiverHCCViral life cycle - HIV-146/402063/84653.25e-051.88e-041.04e-0446
hsa0414432LiverHCCEndocytosis178/4020251/84652.03e-145.22e-132.91e-13178
hsa0325011LiverHCCViral life cycle - HIV-146/402063/84653.25e-051.88e-041.04e-0446
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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
VPS4ASNVMissense_Mutationnovelc.940C>Gp.Leu314Valp.L314VQ9UN37protein_codingdeleterious(0)benign(0.076)TCGA-3C-AALI-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificPoly EComplete Response
VPS4ASNVMissense_Mutationrs757227102c.52G>Ap.Glu18Lysp.E18KQ9UN37protein_codingtolerated(0.11)possibly_damaging(0.595)TCGA-A2-A0YD-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
VPS4ASNVMissense_Mutationc.1135N>Gp.Pro379Alap.P379AQ9UN37protein_codingdeleterious(0.03)possibly_damaging(0.839)TCGA-E2-A1B6-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificAdriamycinSD
VPS4AinsertionNonsense_Mutationnovelc.158_159insCATGGTGAAACTCTGTCTGCACTAAAAATACAAAAATTAGCCp.Lys53delinsAsnMetValLysLeuCysLeuHisTerLysTyrLysAsnTerProp.K53delinsNMVKLCLH*KYKN*PQ9UN37protein_codingTCGA-AQ-A04J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
VPS4AinsertionNonsense_Mutationnovelc.476_477insAGGCTGAAGGGCCAGCTTGTGACTTTCCGTCTp.Trp160GlyfsTer2p.W160Gfs*2Q9UN37protein_codingTCGA-AR-A0TY-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificPaclitaxelPD
VPS4ASNVMissense_Mutationnovelc.733C>Tp.Arg245Trpp.R245WQ9UN37protein_codingdeleterious(0)probably_damaging(1)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
VPS4ASNVMissense_Mutationnovelc.944C>Tp.Thr315Metp.T315MQ9UN37protein_codingdeleterious(0)benign(0.276)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
VPS4ASNVMissense_Mutationc.802N>Tp.Leu268Phep.L268FQ9UN37protein_codingdeleterious(0)probably_damaging(0.996)TCGA-IR-A3LL-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
VPS4ASNVMissense_Mutationc.441N>Gp.Ile147Metp.I147MQ9UN37protein_codingtolerated(0.09)benign(0.097)TCGA-JX-A3Q0-01Cervixcervical & endocervical cancerFemale<65III/IVUnknownUnknownSD
VPS4ASNVMissense_Mutationc.632N>Gp.Asn211Serp.N211SQ9UN37protein_codingtolerated(0.26)benign(0.005)TCGA-AA-3663-01Colorectumcolon 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
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