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: NPHS1

Gene summary for NPHS1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

NPHS1

Gene ID

4868

Gene nameNPHS1 adhesion molecule, nephrin
Gene AliasCNF
Cytomap19q13.12
Gene Typeprotein-coding
GO ID

GO:0000165

UniProtAcc

O60500


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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
4868NPHS1HCC1HumanLiverHCC5.16e-137.78e-010.5336
4868NPHS1HCC2HumanLiverHCC1.40e-262.50e+000.5341
4868NPHS1HCC5HumanLiverHCC2.17e-179.59e-010.4932
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
∗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:004325422LiverHCCregulation of protein-containing complex assembly264/7958428/187235.47e-164.39e-14264
GO:005125822LiverHCCprotein polymerization182/7958297/187234.17e-111.58e-09182
GO:003133412LiverHCCpositive regulation of protein-containing complex assembly150/7958237/187237.35e-112.63e-09150
GO:190290322LiverHCCregulation of supramolecular fiber organization224/7958383/187231.54e-105.33e-09224
GO:000701522LiverHCCactin filament organization252/7958442/187233.83e-101.25e-08252
GO:190290522LiverHCCpositive regulation of supramolecular fiber organization131/7958209/187232.85e-097.69e-08131
GO:005149522LiverHCCpositive regulation of cytoskeleton organization138/7958226/187231.26e-083.12e-07138
GO:003253522LiverHCCregulation of cellular component size217/7958383/187231.28e-083.14e-07217
GO:003227122LiverHCCregulation of protein polymerization141/7958233/187232.00e-084.72e-07141
GO:003297022LiverHCCregulation of actin filament-based process222/7958397/187233.81e-088.30e-07222
GO:003227322LiverHCCpositive regulation of protein polymerization90/7958138/187235.73e-081.21e-0690
GO:003295622LiverHCCregulation of actin cytoskeleton organization202/7958358/187236.18e-081.29e-06202
GO:000815422LiverHCCactin polymerization or depolymerization130/7958218/187232.31e-074.14e-06130
GO:003004122LiverHCCactin filament polymerization116/7958191/187232.66e-074.68e-06116
GO:011005322LiverHCCregulation of actin filament organization158/7958278/187239.01e-071.37e-05158
GO:003083212LiverHCCregulation of actin filament length113/7958189/187231.16e-061.71e-05113
GO:003083322LiverHCCregulation of actin filament polymerization104/7958172/187231.46e-062.08e-05104
GO:000806412LiverHCCregulation of actin polymerization or depolymerization112/7958188/187231.65e-062.31e-05112
GO:003109822LiverHCCstress-activated protein kinase signaling cascade138/7958247/187231.43e-051.57e-04138
GO:005140322LiverHCCstress-activated MAPK cascade134/7958239/187231.50e-051.64e-04134
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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
NPHS1SNVMissense_Mutationc.2819N>Tp.Arg940Leup.R940LO60500protein_codingdeleterious(0.04)benign(0.34)TCGA-AR-A0TQ-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicinSD
NPHS1SNVMissense_Mutationc.3367C>Tp.Arg1123Trpp.R1123WO60500protein_codingtolerated(0.05)benign(0.353)TCGA-BH-A18J-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownPD
NPHS1insertionFrame_Shift_Insnovelc.757_758insAAAATTCTAGTGAAAACCCTCAp.Gly253GlufsTer26p.G253Efs*26O60500protein_codingTCGA-A2-A0EM-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
NPHS1insertionFrame_Shift_Insnovelc.3072_3073insAp.Ala1025SerfsTer2p.A1025Sfs*2O60500protein_codingTCGA-AQ-A04J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
NPHS1insertionFrame_Shift_Insnovelc.3071_3072insCCCAAAGTGTTGGGATTACAGGTGTp.Ala1025ProfsTer10p.A1025Pfs*10O60500protein_codingTCGA-AQ-A04J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
NPHS1deletionFrame_Shift_Delnovelc.476delNp.Asn159ThrfsTer17p.N159Tfs*17O60500protein_codingTCGA-D8-A27V-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenSD
NPHS1insertionFrame_Shift_Insrs386833936c.3250_3251insGp.Val1084GlyfsTer12p.V1084Gfs*12O60500protein_codingTCGA-EW-A6SA-01Breastbreast invasive carcinomaMale<65I/IIUnknownUnknownSD
NPHS1SNVMissense_Mutationnovelc.1181N>Ap.Gly394Aspp.G394DO60500protein_codingdeleterious(0)probably_damaging(1)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
NPHS1SNVMissense_Mutationnovelc.826C>Gp.Leu276Valp.L276VO60500protein_codingdeleterious(0)probably_damaging(0.999)TCGA-C5-A2LY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
NPHS1SNVMissense_Mutationrs781430347c.3263N>Ap.Arg1088Glnp.R1088QO60500protein_codingdeleterious(0.04)benign(0.001)TCGA-C5-A7CG-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
4868NPHS1NAlosartanLOSARTAN
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