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: NPTN

Gene summary for NPTN

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

NPTN

Gene ID

27020

Gene nameneuroplastin
Gene AliasGP55
Cytomap15q24.1
Gene Typeprotein-coding
GO ID

GO:0000165

UniProtAcc

Q9Y639


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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
27020NPTNLZE2DHumanEsophagusHGIN4.96e-035.27e-020.0642
27020NPTNLZE4THumanEsophagusESCC5.95e-081.89e-010.0811
27020NPTNLZE8THumanEsophagusESCC4.02e-021.16e-030.067
27020NPTNLZE24THumanEsophagusESCC1.86e-093.38e-010.0596
27020NPTNLZE21THumanEsophagusESCC8.76e-04-3.89e-030.0655
27020NPTNP2T-EHumanEsophagusESCC6.78e-182.04e-010.1177
27020NPTNP4T-EHumanEsophagusESCC1.78e-215.81e-010.1323
27020NPTNP5T-EHumanEsophagusESCC6.06e-19-7.36e-020.1327
27020NPTNP8T-EHumanEsophagusESCC1.61e-551.52e+000.0889
27020NPTNP9T-EHumanEsophagusESCC7.76e-082.72e-010.1131
27020NPTNP10T-EHumanEsophagusESCC4.18e-316.34e-010.116
27020NPTNP11T-EHumanEsophagusESCC2.18e-162.82e-010.1426
27020NPTNP12T-EHumanEsophagusESCC3.60e-234.26e-010.1122
27020NPTNP15T-EHumanEsophagusESCC1.38e-194.45e-010.1149
27020NPTNP16T-EHumanEsophagusESCC4.79e-141.12e-010.1153
27020NPTNP19T-EHumanEsophagusESCC3.28e-081.37e-010.1662
27020NPTNP20T-EHumanEsophagusESCC1.24e-112.07e-010.1124
27020NPTNP21T-EHumanEsophagusESCC7.58e-213.76e-010.1617
27020NPTNP22T-EHumanEsophagusESCC7.30e-151.88e-010.1236
27020NPTNP23T-EHumanEsophagusESCC6.98e-165.27e-010.108
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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:190382926EsophagusHGINpositive regulation of cellular protein localization75/2587276/187233.19e-092.30e-0775
GO:00315035EsophagusHGINprotein-containing complex localization50/2587220/187232.18e-043.98e-0350
GO:000931418EsophagusHGINresponse to radiation88/2587456/187236.26e-048.65e-0388
GO:00094165EsophagusHGINresponse to light stimulus61/2587320/187235.20e-034.30e-0261
GO:1903829111EsophagusESCCpositive regulation of cellular protein localization199/8552276/187232.99e-193.45e-17199
GO:000931419EsophagusESCCresponse to radiation277/8552456/187234.42e-111.43e-09277
GO:003150314EsophagusESCCprotein-containing complex localization139/8552220/187231.14e-071.85e-06139
GO:003134616EsophagusESCCpositive regulation of cell projection organization201/8552353/187231.19e-051.11e-04201
GO:001072010EsophagusESCCpositive regulation of cell development172/8552298/187231.74e-051.55e-04172
GO:000941611EsophagusESCCresponse to light stimulus183/8552320/187232.03e-051.76e-04183
GO:005076710EsophagusESCCregulation of neurogenesis203/8552364/187236.10e-054.68e-04203
GO:00507697EsophagusESCCpositive regulation of neurogenesis131/8552225/187239.71e-056.90e-04131
GO:006156415EsophagusESCCaxon development251/8552467/187232.41e-041.49e-03251
GO:001097516EsophagusESCCregulation of neuron projection development240/8552445/187232.48e-041.53e-03240
GO:003432918EsophagusESCCcell junction assembly227/8552420/187233.06e-041.83e-03227
GO:00519606EsophagusESCCregulation of nervous system development237/8552443/187235.02e-042.78e-03237
GO:00519625EsophagusESCCpositive regulation of nervous system development149/8552272/187231.50e-037.06e-03149
GO:000740915EsophagusESCCaxonogenesis219/8552418/187233.14e-031.31e-02219
GO:00109764EsophagusESCCpositive regulation of neuron projection development91/8552163/187235.72e-032.13e-0291
GO:190382912LiverCirrhoticpositive regulation of cellular protein localization123/4634276/187234.06e-133.22e-11123
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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
NPTNSNVMissense_Mutationc.712N>Tp.Pro238Serp.P238SQ9Y639protein_codingdeleterious(0)probably_damaging(0.997)TCGA-A2-A04W-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
NPTNSNVMissense_Mutationnovelc.673N>Ap.Ala225Thrp.A225TQ9Y639protein_codingtolerated(0.42)possibly_damaging(0.537)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
NPTNSNVMissense_Mutationc.118G>Cp.Glu40Glnp.E40QQ9Y639protein_codingtolerated(1)probably_damaging(0.998)TCGA-DS-A0VM-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinPD
NPTNSNVMissense_Mutationnovelc.782N>Tp.Ser261Leup.S261LQ9Y639protein_codingdeleterious(0)probably_damaging(0.978)TCGA-EA-A1QS-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
NPTNSNVMissense_Mutationc.527N>Ap.Ser176Tyrp.S176YQ9Y639protein_codingtolerated(0.47)benign(0.186)TCGA-AA-A02H-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownPD
NPTNSNVMissense_Mutationc.1025N>Ap.Pro342Hisp.P342HQ9Y639protein_codingdeleterious(0)probably_damaging(0.999)TCGA-AD-6889-01Colorectumcolon adenocarcinomaMale>=65I/IIChemotherapyxelodaPD
NPTNSNVMissense_Mutationnovelc.193N>Cp.Trp65Argp.W65RQ9Y639protein_codingdeleterious(0)probably_damaging(0.999)TCGA-AD-6889-01Colorectumcolon adenocarcinomaMale>=65I/IIChemotherapyxelodaPD
NPTNSNVMissense_Mutationc.418N>Ap.Ala140Thrp.A140TQ9Y639protein_codingdeleterious(0)possibly_damaging(0.494)TCGA-D5-6930-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
NPTNSNVMissense_Mutationnovelc.1046A>Cp.Glu349Alap.E349AQ9Y639protein_codingdeleterious(0)probably_damaging(0.997)TCGA-AG-3892-01Colorectumrectum adenocarcinomaFemale<65I/IIUnknownUnknownSD
NPTNSNVMissense_Mutationc.527C>Tp.Ser176Phep.S176FQ9Y639protein_codingtolerated(0.27)possibly_damaging(0.505)TCGA-AG-A026-01Colorectumrectum adenocarcinomaMale>=65I/IIUnknownUnknownPD
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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
27020NPTNCELL SURFACE, DRUGGABLE GENOMEANTISERUM9004047
27020NPTNCELL SURFACE, DRUGGABLE GENOMEGP1008779689
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