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: VAMP2

Gene summary for VAMP2

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

VAMP2

Gene ID

6844

Gene namevesicle associated membrane protein 2
Gene AliasNEDHAHM
Cytomap17p13.1
Gene Typeprotein-coding
GO ID

GO:0001505

UniProtAcc

F8WCA0


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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
6844VAMP2GSM4909281HumanBreastIDC1.05e-02-2.22e-010.21
6844VAMP2GSM4909282HumanBreastIDC5.23e-05-2.97e-01-0.0288
6844VAMP2GSM4909285HumanBreastIDC6.25e-10-3.86e-010.21
6844VAMP2GSM4909286HumanBreastIDC8.68e-04-1.76e-010.1081
6844VAMP2GSM4909287HumanBreastIDC9.85e-23-4.86e-010.2057
6844VAMP2GSM4909290HumanBreastIDC1.70e-11-4.22e-010.2096
6844VAMP2GSM4909291HumanBreastIDC7.38e-04-2.87e-010.1753
6844VAMP2GSM4909294HumanBreastIDC5.81e-17-4.32e-010.2022
6844VAMP2GSM4909296HumanBreastIDC5.76e-15-3.67e-010.1524
6844VAMP2GSM4909297HumanBreastIDC2.97e-15-1.23e-010.1517
6844VAMP2GSM4909301HumanBreastIDC3.64e-022.59e-010.1577
6844VAMP2GSM4909304HumanBreastIDC1.28e-05-3.39e-010.1636
6844VAMP2GSM4909305HumanBreastIDC3.89e-044.07e-010.0436
6844VAMP2GSM4909309HumanBreastIDC4.88e-021.04e-010.0483
6844VAMP2GSM4909311HumanBreastIDC7.88e-31-3.42e-010.1534
6844VAMP2GSM4909312HumanBreastIDC4.84e-12-1.12e-010.1552
6844VAMP2GSM4909313HumanBreastIDC5.43e-173.95e-010.0391
6844VAMP2GSM4909315HumanBreastIDC1.22e-12-4.17e-010.21
6844VAMP2GSM4909316HumanBreastIDC6.21e-09-4.33e-010.21
6844VAMP2GSM4909319HumanBreastIDC2.88e-40-3.15e-010.1563
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
BreastThe 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.IDC: Invasive ductal carcinoma
DCIS: Ductal carcinoma in situ
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:000974624Oral cavityNEOLPresponse to hexose39/2005219/187231.00e-037.68e-0339
GO:009887631Oral cavityNEOLPvesicle-mediated transport to the plasma membrane26/2005136/187232.40e-031.53e-0226
GO:000974923Oral cavityNEOLPresponse to glucose36/2005212/187233.52e-032.07e-0236
GO:003150331Oral cavityNEOLPprotein-containing complex localization37/2005220/187233.69e-032.15e-0237
GO:00109598Oral cavityNEOLPregulation of metal ion transport59/2005406/187239.36e-034.44e-0259
GO:004819310ProstateBPHGolgi vesicle transport102/3107296/187233.90e-144.56e-12102
GO:003238610ProstateBPHregulation of intracellular transport106/3107337/187238.77e-126.70e-10106
GO:190495117ProstateBPHpositive regulation of establishment of protein localization101/3107319/187231.77e-111.24e-09101
GO:007265916ProstateBPHprotein localization to plasma membrane89/3107284/187235.00e-102.56e-0889
GO:003315716ProstateBPHregulation of intracellular protein transport76/3107229/187235.05e-102.56e-0876
GO:005122217ProstateBPHpositive regulation of protein transport93/3107303/187236.94e-103.25e-0893
GO:003238816ProstateBPHpositive regulation of intracellular transport68/3107202/187232.08e-098.35e-0868
GO:190165310ProstateBPHcellular response to peptide104/3107359/187232.51e-091.00e-07104
GO:199077810ProstateBPHprotein localization to cell periphery95/3107333/187232.78e-088.13e-0795
GO:00903169ProstateBPHpositive regulation of intracellular protein transport55/3107160/187233.09e-088.91e-0755
GO:009015016ProstateBPHestablishment of protein localization to membrane77/3107260/187231.06e-072.56e-0677
GO:004343417ProstateBPHresponse to peptide hormone109/3107414/187232.73e-075.91e-06109
GO:00713759ProstateBPHcellular response to peptide hormone stimulus82/3107290/187233.65e-077.65e-0682
GO:003286910ProstateBPHcellular response to insulin stimulus61/3107203/187231.26e-062.20e-0561
GO:00160507ProstateBPHvesicle organization82/3107300/187231.64e-062.78e-0582
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa049704BreastIDCSalivary secretion18/86793/84655.69e-033.13e-022.34e-0218
hsa0497011BreastIDCSalivary secretion18/86793/84655.69e-033.13e-022.34e-0218
hsa04962ColorectumADVasopressin-regulated water reabsorption19/209244/84655.48e-032.48e-021.58e-0219
hsa049621ColorectumADVasopressin-regulated water reabsorption19/209244/84655.48e-032.48e-021.58e-0219
hsa049622ColorectumMSSVasopressin-regulated water reabsorption17/187544/84659.76e-033.55e-022.18e-0217
hsa049623ColorectumMSSVasopressin-regulated water reabsorption17/187544/84659.76e-033.55e-022.18e-0217
hsa049627EsophagusHGINVasopressin-regulated water reabsorption14/138344/84658.21e-034.71e-023.74e-0214
hsa0496214EsophagusHGINVasopressin-regulated water reabsorption14/138344/84658.21e-034.71e-023.74e-0214
hsa041305EsophagusESCCSNARE interactions in vesicular transport28/420533/84652.75e-051.32e-046.75e-0528
hsa0496223EsophagusESCCVasopressin-regulated water reabsorption33/420544/84655.27e-041.78e-039.13e-0433
hsa0413012EsophagusESCCSNARE interactions in vesicular transport28/420533/84652.75e-051.32e-046.75e-0528
hsa0496233EsophagusESCCVasopressin-regulated water reabsorption33/420544/84655.27e-041.78e-039.13e-0433
hsa04130LiverCirrhoticSNARE interactions in vesicular transport18/253033/84652.64e-031.10e-026.76e-0318
hsa041301LiverCirrhoticSNARE interactions in vesicular transport18/253033/84652.64e-031.10e-026.76e-0318
hsa041302LiverHCCSNARE interactions in vesicular transport25/402033/84658.78e-043.38e-031.88e-0325
hsa041303LiverHCCSNARE interactions in vesicular transport25/402033/84658.78e-043.38e-031.88e-0325
hsa041304Oral cavityOSCCSNARE interactions in vesicular transport28/370433/84651.31e-067.18e-063.66e-0628
hsa049626Oral cavityOSCCVasopressin-regulated water reabsorption29/370444/84652.47e-036.52e-033.32e-0329
hsa0413011Oral cavityOSCCSNARE interactions in vesicular transport28/370433/84651.31e-067.18e-063.66e-0628
hsa0496213Oral cavityOSCCVasopressin-regulated water reabsorption29/370444/84652.47e-036.52e-033.32e-0329
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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
VAMP2SNVMissense_Mutationc.175N>Ap.Asp59Asnp.D59Nprotein_codingdeleterious(0)probably_damaging(0.984)TCGA-AD-6895-01Colorectumcolon adenocarcinomaMale>=65III/IVUnknownUnknownSD
VAMP2SNVMissense_Mutationnovelc.96G>Tp.Arg32Serp.R32Sprotein_codingdeleterious(0)benign(0.248)TCGA-B5-A1MX-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIHormone TherapymegaceSD
VAMP2SNVMissense_Mutationnovelc.136N>Ap.Asp46Asnp.D46Nprotein_codingdeleterious(0.02)benign(0.135)TCGA-DF-A2KN-01Endometriumuterine corpus endometrioid carcinomaFemaleUnknownI/IIUnknownUnknownSD
VAMP2SNVMissense_Mutationnovelc.95N>Tp.Arg32Metp.R32Mprotein_codingdeleterious(0)possibly_damaging(0.746)TCGA-EO-A22R-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
VAMP2SNVMissense_Mutationnovelc.28N>Cp.Ala10Prop.A10Pprotein_codingtolerated_low_confidence(0.2)benign(0)TCGA-PG-A6IB-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
VAMP2insertionNonsense_Mutationnovelc.3_4insAAACTCTGTCTCTACTAAAAAAATACAAAATTAGCCGGGTp.Asp2LysfsTer6p.D2Kfs*6protein_codingTCGA-AX-A3FS-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
VAMP2insertionFrame_Shift_Insrs774244975c.35_36insCp.Ala13CysfsTer19p.A13Cfs*19protein_codingTCGA-DF-A2KN-01Endometriumuterine corpus endometrioid carcinomaFemaleUnknownI/IIUnknownUnknownSD
VAMP2insertionFrame_Shift_Insrs774244975c.35_36insCp.Ala13CysfsTer19p.A13Cfs*19protein_codingTCGA-VQ-A91K-01Stomachstomach adenocarcinomaMale>=65III/IVChemotherapyfluorouracilCR
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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
6844VAMP2DRUGGABLE GENOMEBOTULINUM TOXIN TYPE B
6844VAMP2DRUGGABLE GENOMEPMA17196367
6844VAMP2DRUGGABLE GENOMEINSULININSULIN7796801,9267469,9430681,8973549
6844VAMP2DRUGGABLE GENOMEinhibitorCHEMBL1201569BOTULINUM TOXIN TYPE B
6844VAMP2DRUGGABLE GENOMEBOTULINUM TOXIN TYPE B
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