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: VILL

Gene summary for VILL

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

VILL

Gene ID

50853

Gene namevillin like
Gene AliasVILL
Cytomap3p22.2
Gene Typeprotein-coding
GO ID

GO:0006996

UniProtAcc

O15195


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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
50853VILLHTA11_2487_2000001011HumanColorectumSER1.90e-107.84e-01-0.1808
50853VILLHTA11_347_2000001011HumanColorectumAD5.99e-083.84e-01-0.1954
50853VILLHTA11_411_2000001011HumanColorectumSER1.95e-081.69e+00-0.2602
50853VILLHTA11_2112_2000001011HumanColorectumSER2.06e-058.20e-01-0.2196
50853VILLHTA11_696_2000001011HumanColorectumAD7.85e-094.98e-01-0.1464
50853VILLHTA11_866_2000001011HumanColorectumAD3.78e-052.89e-01-0.1001
50853VILLHTA11_2992_2000001011HumanColorectumSER8.74e-046.84e-01-0.1706
50853VILLLZE24THumanEsophagusESCC2.42e-133.15e-010.0596
50853VILLP4T-EHumanEsophagusESCC2.20e-021.08e-010.1323
50853VILLP8T-EHumanEsophagusESCC9.16e-091.94e-010.0889
50853VILLP10T-EHumanEsophagusESCC1.91e-044.02e-020.116
50853VILLP12T-EHumanEsophagusESCC1.07e-035.07e-020.1122
50853VILLP16T-EHumanEsophagusESCC3.71e-078.61e-020.1153
50853VILLP20T-EHumanEsophagusESCC3.11e-041.06e-010.1124
50853VILLP21T-EHumanEsophagusESCC2.89e-055.25e-020.1617
50853VILLP27T-EHumanEsophagusESCC1.83e-046.05e-020.1055
50853VILLP28T-EHumanEsophagusESCC2.20e-071.25e-010.1149
50853VILLP36T-EHumanEsophagusESCC5.72e-041.84e-010.1187
50853VILLP39T-EHumanEsophagusESCC3.23e-044.92e-020.0894
50853VILLP57T-EHumanEsophagusESCC1.03e-059.67e-020.0926
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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
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
∗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:0007015ColorectumADactin filament organization167/3918442/187231.65e-167.94e-14167
GO:0032535ColorectumADregulation of cellular component size142/3918383/187231.74e-133.41e-11142
GO:1902903ColorectumADregulation of supramolecular fiber organization139/3918383/187232.01e-123.19e-10139
GO:0032970ColorectumADregulation of actin filament-based process142/3918397/187234.05e-125.90e-10142
GO:0110053ColorectumADregulation of actin filament organization108/3918278/187235.02e-126.98e-10108
GO:0008154ColorectumADactin polymerization or depolymerization90/3918218/187236.14e-128.23e-1090
GO:0032271ColorectumADregulation of protein polymerization94/3918233/187231.01e-111.29e-0994
GO:0030041ColorectumADactin filament polymerization81/3918191/187231.35e-111.69e-0981
GO:0051258ColorectumADprotein polymerization112/3918297/187231.85e-112.27e-09112
GO:0043254ColorectumADregulation of protein-containing complex assembly148/3918428/187232.64e-113.18e-09148
GO:0008064ColorectumADregulation of actin polymerization or depolymerization79/3918188/187234.17e-114.74e-0979
GO:0030833ColorectumADregulation of actin filament polymerization74/3918172/187234.50e-115.03e-0974
GO:0030832ColorectumADregulation of actin filament length79/3918189/187235.71e-116.27e-0979
GO:0032956ColorectumADregulation of actin cytoskeleton organization127/3918358/187231.03e-101.04e-08127
GO:0022411ColorectumADcellular component disassembly147/3918443/187238.53e-106.76e-08147
GO:0032984ColorectumADprotein-containing complex disassembly81/3918224/187239.41e-084.65e-0681
GO:0010639ColorectumADnegative regulation of organelle organization114/3918348/187231.41e-076.49e-06114
GO:0032272ColorectumADnegative regulation of protein polymerization36/391880/187231.13e-063.72e-0536
GO:0030837ColorectumADnegative regulation of actin filament polymerization30/391865/187234.59e-061.22e-0430
GO:1902904ColorectumADnegative regulation of supramolecular fiber organization60/3918167/187235.23e-061.35e-0460
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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
VILLSNVMissense_Mutationrs140199753c.2141N>Tp.Pro714Leup.P714LO15195protein_codingtolerated(0.05)benign(0)TCGA-A2-A1FW-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycytoxanSD
VILLSNVMissense_Mutationnovelc.895N>Ap.Arg299Serp.R299SO15195protein_codingdeleterious(0.02)possibly_damaging(0.73)TCGA-A7-A0DA-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
VILLSNVMissense_Mutationrs754145754c.2413G>Cp.Ala805Prop.A805PO15195protein_codingtolerated(0.2)benign(0.005)TCGA-AR-A24Q-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
VILLSNVMissense_Mutationc.1369G>Ap.Glu457Lysp.E457KO15195protein_codingtolerated(0.14)benign(0.003)TCGA-B6-A0RS-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownPD
VILLSNVMissense_Mutationc.881N>Gp.Tyr294Cysp.Y294CO15195protein_codingdeleterious(0)probably_damaging(0.996)TCGA-BH-A18G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
VILLSNVMissense_Mutationnovelc.793N>Tp.Val265Phep.V265FO15195protein_codingdeleterious(0.01)benign(0.044)TCGA-OL-A5RW-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinCR
VILLSNVMissense_Mutationnovelc.1905G>Tp.Glu635Aspp.E635DO15195protein_codingtolerated(1)benign(0.013)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
VILLSNVMissense_Mutationrs372162890c.1994C>Tp.Ala665Valp.A665VO15195protein_codingdeleterious(0.05)probably_damaging(0.941)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
VILLSNVMissense_Mutationrs200122241c.2221C>Tp.Arg741Trpp.R741WO15195protein_codingdeleterious(0.02)possibly_damaging(0.586)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
VILLSNVMissense_Mutationc.1222N>Tp.Pro408Serp.P408SO15195protein_codingtolerated(0.21)benign(0.088)TCGA-EK-A2PG-01Cervixcervical & endocervical cancerFemale>=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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