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| TissGeneSummary for NPHS2 |
 Gene summary |
| Basic gene information | Gene symbol | NPHS2 |
| Gene name | nephrosis 2, idiopathic, steroid-resistant (podocin) | |
| Synonyms | PDCN|SRN1 | |
| Cytomap | UCSC genome browser: 1q25.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001297575.1, NM_014625.3, | |
| Description | podocin | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 604766 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000116218 | ||
| HPRD : 05303 | ||
| Vega : OTTHUMG00000035252 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_NPHS2 | |
| BioGPS: 7827 | ||
| Pathway | NCI Pathway Interaction Database: NPHS2 | |
| KEGG: NPHS2 | ||
| REACTOME: NPHS2 | ||
| Pathway Commons: NPHS2 | ||
| Context | iHOP: NPHS2 | |
| ligand binding site mutation search in PubMed: NPHS2 | ||
| UCL Cancer Institute: NPHS2 | ||
| Assigned class in TissGDB* | A | |
| Included tissue-specific gene expression resources | HPA,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 NPHS2 | Human 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. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID | GO:0031532 | actin cytoskeleton reorganization | 17675666 | GO:0031532 | actin cytoskeleton reorganization | 17675666 |
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| TissGeneExp for NPHS2 |
| 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) |
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| 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) |
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| 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. |
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| 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) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| KIRP | 0.806559306 | 8.953353056 | -8.14679375 | 4.66E-13 | 8.10E-12 |
| KICH | -0.272337319 | 7.890734681 | -8.163072 | 7.43E-11 | 5.95E-10 |
| KIRC | 0.639427015 | 7.902188126 | -7.262761111 | 3.40E-19 | 2.49E-18 |
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| TissGene-miRNA for NPHS2 |
| 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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for NPHS2 |
| TissGeneSNV for NPHS2 |
| 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. |
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| 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) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.S109F | SKCM | 2 |
| p.L235F | LUAD | 1 |
| p.G140E | SKCM | 1 |
| p.A242T | STAD | 1 |
| p.R58G | HNSC | 1 |
| p.R15X | STAD | 1 |
| p.V218M | UCEC | 1 |
| p.P118L | SKCM | 1 |
| p.I136V | LUAD | 1 |
| p.G359E | SKCM | 1 |
| p.R229G | CESC | 1 |
| p.H177P | LUSC | 1 |
| p.R138X | SKCM | 1 |
| p.G149D | SKCM | 1 |
| p.V260L | UCEC | 1 |
| p.R138* | SKCM | 1 |
| p.E56K | SKCM | 1 |
| p.A279S | LUAD | 1 |
| p.K94T | LUAD | 1 |
| p.L152I | STAD | 1 |
| p.G74S | STAD | 1 |
| p.A41T | LIHC | 1 |
| p.W103L | HNSC | 1 |
| p.I258M | HNSC | 1 |
| p.P175H | UCEC | 1 |
| p.P364R | LUAD | 1 |
| p.V180M | ESCA | 1 |
| p.Q328K | ESCA | 1 |
| p.L312P | LUAD | 1 |
| p.L327F | SKCM | 1 |
| p.E310Q | BLCA | 1 |
| p.S95F | SKCM | 1 |
| p.E130* | LUAD | 1 |
| p.D244Y | UCEC | 1 |
| p.Q129H | THYM | 1 |
| p.P316A | LUAD | 1 |
| p.L330P | BLCA | 1 |
| p.A242T | LGG | 1 |
| p.P369L | HNSC | 1 |
| p.W256* | SKCM | 1 |
| p.S109F | UCEC | 1 |
| p.P364Q | LUAD | 1 |
| p.E102K | SARC | 1 |
| p.L235I | UCEC | 1 |
| p.M222I | SKCM | 1 |
| p.R88L | HNSC | 1 |
| p.R196Q | READ | 1 |
| p.A248T | BRCA | 1 |
| p.V125L | LUAD | 1 |
| p.V125I | PAAD | 1 |
| p.A191D | LUSC | 1 |
| p.Q219* | BLCA | 1 |
| p.W256X | SKCM | 1 |
| p.P144T | PAAD | 1 |
| p.D379N | LUSC | 1 |
| p.L104I | HNSC | 1 |
| p.P369L | SKCM | 1 |
| p.R229X | READ | 1 |
| p.Y131N | LUAD | 1 |
| p.Q328* | LUAD | 1 |
| p.L107V | ESCA | 1 |
| p.L361P | GBM | 1 |
| p.R229Q | COAD | 1 |
| p.R196Q | COAD | 1 |
| p.P341L | SKCM | 1 |
| p.P20L | THCA | 1 |
| p.E281K | SKCM | 1 |
| p.T357N | UCEC | 1 |
| p.R168C | SKCM | 1 |
| p.T116N | ESCA | 1 |
| p.G92C | LUAD | 1 |
| p.D244H | OV | 1 |
| p.P364T | LUAD | 1 |
| p.S313P | COAD | 1 |
| p.S120F | SKCM | 1 |
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| TissGeneCNV for NPHS2 |
| 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) |
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| TissGeneFusions for NPHS2 |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
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| TissGeneNet for NPHS2 |
| 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) |
 |  |
| 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 |
| 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. |
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| 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. |
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| 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. |
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| 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. |
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| TissGeneClin for NPHS2 |
| TissGeneDrug for NPHS2 |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for NPHS2 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0027726 | Nephrotic Syndrome | 73 | BeFree,CTD_human,GAD,LHGDN,RGD |
| umls:C0403397 | Steroid-resistant nephrotic syndrome | 68 | BeFree |
| umls:C0017668 | Focal glomerulosclerosis | 41 | BeFree,CTD_human,GAD,LHGDN |
| umls:C0333497 | Segmental glomerulosclerosis | 23 | BeFree |
| umls:C0022658 | Kidney Diseases | 17 | BeFree,GAD |
| umls:C0022661 | Kidney Failure, Chronic | 17 | BeFree,GAD,LHGDN |
| umls:C3496337 | Nephrotic Syndrome, Idiopathic | 9 | MGD,UNIPROT |
| umls:C0035078 | Kidney Failure | 8 | BeFree |
| umls:C2316810 | Chronic kidney disease stage 5 | 8 | BeFree |
| umls:C0268731 | Renal glomerular disease | 6 | BeFree |
| umls:C0011881 | Diabetic Nephropathy | 5 | BeFree,GAD,LHGDN |
| umls:C0017661 | IGA Glomerulonephritis | 5 | BeFree |
| umls:C0027720 | Nephrosis | 5 | BeFree,CTD_human,GAD |
| umls:C1704321 | Nephrotic Syndrome, Minimal Change | 5 | BeFree |
| umls:C1704320 | Glomerulonephritis, Minimal Change | 4 | BeFree |
| umls:C0001925 | Albuminuria | 3 | CTD_human,GAD |
| umls:C0027721 | Lipoid nephrosis | 3 | BeFree |
| umls:C0033687 | Proteinuria | 3 | CLINVAR,GAD,RGD |
| umls:C1709661 | Primary Focal Segmental Glomerulosclerosis | 3 | BeFree |
| umls:C0017665 | Membranous glomerulonephritis | 2 | BeFree,RGD |
| umls:C0020538 | Hypertensive disease | 2 | GAD |
| umls:C0027697 | Nephritis | 2 | BeFree,LHGDN |
| umls:C0178664 | Glomerulosclerosis (disorder) | 2 | BeFree |
| umls:C0265962 | Ichthyosis linearis circumflexa | 2 | BeFree |
| umls:C0268732 | Nephritic syndrome | 2 | BeFree |
| umls:C0268747 | Diffuse mesangial sclerosis (disorder) | 2 | BeFree |
| umls:C0403396 | Steroid-sensitive nephrotic syndrome | 2 | BeFree |
| umls:C0403447 | Chronic Kidney Insufficiency | 2 | BeFree |
| umls:C0730345 | Microalbuminuria | 2 | BeFree |
| umls:C1868672 | NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE | 2 | CLINVAR,CTD_human |
| umls:C0002726 | Amyloidosis | 1 | BeFree |
| umls:C0003850 | Arteriosclerosis | 1 | BeFree |
| umls:C0004153 | Atherosclerosis | 1 | BeFree |
| umls:C0004509 | Azoospermia | 1 | BeFree |
| umls:C0011847 | Diabetes | 1 | BeFree |
| umls:C0011849 | Diabetes Mellitus | 1 | BeFree |
| umls:C0011854 | Diabetes Mellitus, Insulin-Dependent | 1 | BeFree,GAD |
| umls:C0012546 | Diphtheria | 1 | BeFree |
| umls:C0015397 | Disorder of eye | 1 | GAD |
| umls:C0018799 | Heart Diseases | 1 | BeFree |
| umls:C0019693 | HIV Infections | 1 | BeFree |
| umls:C0027708 | Nephroblastoma | 1 | BeFree |
| umls:C0027719 | Nephrosclerosis | 1 | BeFree |
| umls:C0034150 | Purpura | 1 | LHGDN |
| umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
| umls:C0078911 | AIDS-Associated Nephropathy | 1 | GAD |
| umls:C0151744 | Myocardial Ischemia | 1 | BeFree |
| umls:C0342793 | Malonic aciduria | 1 | BeFree |
| umls:C0403398 | Steroid-dependent nephrotic syndrome | 1 | BeFree |
| umls:C0403399 | Finnish congenital nephrotic syndrome | 1 | BeFree |
| umls:C0403440 | Thin basement membrane disease | 1 | BeFree |
| umls:C0445118 | Nephrotic range proteinuria | 1 | BeFree |
| umls:C1305904 | Familial hematuria | 1 | BeFree |
| umls:C1384583 | Congenital absence of germinal epithelium of testes | 1 | BeFree |
| umls:C1636149 | Macular dystrophy, corneal type 1 | 1 | BeFree |
| umls:C1962972 | Proteinuria Adverse Event | 1 | GAD |
| umls:C3825926 | Nephrotic syndrome in children | 1 | BeFree |
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