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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for NPHS2
check button Gene summary
Basic gene informationGene symbolNPHS2
Gene namenephrosis 2, idiopathic, steroid-resistant (podocin)
SynonymsPDCN|SRN1
CytomapUCSC genome browser: 1q25.2
Type of geneprotein-coding
RefGenesNM_001297575.1,
NM_014625.3,
Descriptionpodocin
Modification date20141207
dbXrefs MIM : 604766
HGNC : HGNC
Ensembl : ENSG00000116218
HPRD : 05303
Vega : OTTHUMG00000035252
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NPHS2
BioGPS: 7827
PathwayNCI Pathway Interaction Database: NPHS2
KEGG: NPHS2
REACTOME: NPHS2
Pathway Commons: NPHS2
ContextiHOP: NPHS2
ligand binding site mutation search in PubMed: NPHS2
UCL Cancer Institute: NPHS2
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Kidney
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)KIRC,KIRP,KICH
Reference showing the relevant tissue of NPHS2Human Urine-Derived Renal Progenitors for Personalized Modeling of Genetic Kidney Disorders. Lazzeri E, Ronconi E, Angelotti ML, Peired A, Mazzinghi B, Becherucci F, Conti S, Sansavini G, Sisti A, Ravaglia F, Lombardi D, Provenzano A, Manonelles A, Cruzado JM, Giglio S, Roperto RM, Materassi M, Lasagni L, Romagnani P. J Am Soc Nephrol. 2015 Aug;26(8):1961-74. doi: 10.1681/ASN.2014010057. Epub 2015 Jan 7. (pmid:25568173)
go to article
Description by TissGene annotations
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0031532actin cytoskeleton reorganization17675666
GO:0031532actin cytoskeleton reorganization17675666


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TissGeneExp for NPHS2

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
KIRP0.8065593068.953353056-8.146793754.66E-138.10E-12
KICH-0.2723373197.890734681-8.1630727.43E-115.95E-10
KIRC0.6394270157.902188126-7.2627611113.40E-192.49E-18


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TissGene-miRNA for NPHS2

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for NPHS2
TissGeneSNV for NPHS2

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.S109FSKCM2
p.L235FLUAD1
p.G140ESKCM1
p.A242TSTAD1
p.R58GHNSC1
p.R15XSTAD1
p.V218MUCEC1
p.P118LSKCM1
p.I136VLUAD1
p.G359ESKCM1
p.R229GCESC1
p.H177PLUSC1
p.R138XSKCM1
p.G149DSKCM1
p.V260LUCEC1
p.R138*SKCM1
p.E56KSKCM1
p.A279SLUAD1
p.K94TLUAD1
p.L152ISTAD1
p.G74SSTAD1
p.A41TLIHC1
p.W103LHNSC1
p.I258MHNSC1
p.P175HUCEC1
p.P364RLUAD1
p.V180MESCA1
p.Q328KESCA1
p.L312PLUAD1
p.L327FSKCM1
p.E310QBLCA1
p.S95FSKCM1
p.E130*LUAD1
p.D244YUCEC1
p.Q129HTHYM1
p.P316ALUAD1
p.L330PBLCA1
p.A242TLGG1
p.P369LHNSC1
p.W256*SKCM1
p.S109FUCEC1
p.P364QLUAD1
p.E102KSARC1
p.L235IUCEC1
p.M222ISKCM1
p.R88LHNSC1
p.R196QREAD1
p.A248TBRCA1
p.V125LLUAD1
p.V125IPAAD1
p.A191DLUSC1
p.Q219*BLCA1
p.W256XSKCM1
p.P144TPAAD1
p.D379NLUSC1
p.L104IHNSC1
p.P369LSKCM1
p.R229XREAD1
p.Y131NLUAD1
p.Q328*LUAD1
p.L107VESCA1
p.L361PGBM1
p.R229QCOAD1
p.R196QCOAD1
p.P341LSKCM1
p.P20LTHCA1
p.E281KSKCM1
p.T357NUCEC1
p.R168CSKCM1
p.T116NESCA1
p.G92CLUAD1
p.D244HOV1
p.P364TLUAD1
p.S313PCOAD1
p.S120FSKCM1


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TissGeneCNV for NPHS2

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for NPHS2

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP


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TissGeneNet for NPHS2

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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COAD (tumor)COAD (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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HNSC (tumor)HNSC (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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KICH (tumor)KICH (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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KIRC (tumor)KIRC (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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KIRP (tumor)KIRP (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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LIHC (tumor)LIHC (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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LUAD (tumor)LUAD (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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LUSC (tumor)LUSC (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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PRAD (tumor)PRAD (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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STAD (tumor)STAD (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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THCA (tumor)THCA (normal)
NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (tumor)NPHS2, SH3KBP1, UBC, CD2AP, LMX1B, NPHS1, KIRREL, KIRREL3 (normal)
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TissGeneProg for NPHS2

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for NPHS2
TissGeneDrug for NPHS2

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for NPHS2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0027726Nephrotic Syndrome73BeFree,CTD_human,GAD,LHGDN,RGD
umls:C0403397Steroid-resistant nephrotic syndrome68BeFree
umls:C0017668Focal glomerulosclerosis41BeFree,CTD_human,GAD,LHGDN
umls:C0333497Segmental glomerulosclerosis23BeFree
umls:C0022658Kidney Diseases17BeFree,GAD
umls:C0022661Kidney Failure, Chronic17BeFree,GAD,LHGDN
umls:C3496337Nephrotic Syndrome, Idiopathic9MGD,UNIPROT
umls:C0035078Kidney Failure8BeFree
umls:C2316810Chronic kidney disease stage 58BeFree
umls:C0268731Renal glomerular disease6BeFree
umls:C0011881Diabetic Nephropathy5BeFree,GAD,LHGDN
umls:C0017661IGA Glomerulonephritis5BeFree
umls:C0027720Nephrosis5BeFree,CTD_human,GAD
umls:C1704321Nephrotic Syndrome, Minimal Change5BeFree
umls:C1704320Glomerulonephritis, Minimal Change4BeFree
umls:C0001925Albuminuria3CTD_human,GAD
umls:C0027721Lipoid nephrosis3BeFree
umls:C0033687Proteinuria3CLINVAR,GAD,RGD
umls:C1709661Primary Focal Segmental Glomerulosclerosis3BeFree
umls:C0017665Membranous glomerulonephritis2BeFree,RGD
umls:C0020538Hypertensive disease2GAD
umls:C0027697Nephritis2BeFree,LHGDN
umls:C0178664Glomerulosclerosis (disorder)2BeFree
umls:C0265962Ichthyosis linearis circumflexa2BeFree
umls:C0268732Nephritic syndrome2BeFree
umls:C0268747Diffuse mesangial sclerosis (disorder)2BeFree
umls:C0403396Steroid-sensitive nephrotic syndrome2BeFree
umls:C0403447Chronic Kidney Insufficiency2BeFree
umls:C0730345Microalbuminuria2BeFree
umls:C1868672NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE2CLINVAR,CTD_human
umls:C0002726Amyloidosis1BeFree
umls:C0003850Arteriosclerosis1BeFree
umls:C0004153Atherosclerosis1BeFree
umls:C0004509Azoospermia1BeFree
umls:C0011847Diabetes1BeFree
umls:C0011849Diabetes Mellitus1BeFree
umls:C0011854Diabetes Mellitus, Insulin-Dependent1BeFree,GAD
umls:C0012546Diphtheria1BeFree
umls:C0015397Disorder of eye1GAD
umls:C0018799Heart Diseases1BeFree
umls:C0019693HIV Infections1BeFree
umls:C0027708Nephroblastoma1BeFree
umls:C0027719Nephrosclerosis1BeFree
umls:C0034150Purpura1LHGDN
umls:C0040336Tobacco Use Disorder1GAD
umls:C0078911AIDS-Associated Nephropathy1GAD
umls:C0151744Myocardial Ischemia1BeFree
umls:C0342793Malonic aciduria1BeFree
umls:C0403398Steroid-dependent nephrotic syndrome1BeFree
umls:C0403399Finnish congenital nephrotic syndrome1BeFree
umls:C0403440Thin basement membrane disease1BeFree
umls:C0445118Nephrotic range proteinuria1BeFree
umls:C1305904Familial hematuria1BeFree
umls:C1384583Congenital absence of germinal epithelium of testes1BeFree
umls:C1636149Macular dystrophy, corneal type 11BeFree
umls:C1962972Proteinuria Adverse Event1GAD
umls:C3825926Nephrotic syndrome in children1BeFree