TissGeneSummary for CDH4 |
Gene summary |
Basic gene information | Gene symbol | CDH4 |
Gene name | cadherin 4, type 1, R-cadherin (retinal) | |
Synonyms | CAD4|R-CAD|RCAD | |
Cytomap | UCSC genome browser: 20q13.3 | |
Type of gene | protein-coding | |
RefGenes | NM_001252338.2, NM_001252339.2,NM_001794.4, | |
Description | R-cadherincadherin 4, type 1, preproproteincadherin-4retinal cadherin | |
Modification date | 20141207 | |
dbXrefs | MIM : 603006 | |
HGNC : HGNC | ||
Ensembl : ENSG00000179242 | ||
HPRD : 04304 | ||
Vega : OTTHUMG00000032890 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CDH4 | |
BioGPS: 1002 | ||
Pathway | NCI Pathway Interaction Database: CDH4 | |
KEGG: CDH4 | ||
REACTOME: CDH4 | ||
Pathway Commons: CDH4 | ||
Context | iHOP: CDH4 | |
ligand binding site mutation search in PubMed: CDH4 | ||
UCL Cancer Institute: CDH4 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | OvaryEye | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | OVUVM | |
Reference showing the relevant tissue of CDH4 | ||
Description by TissGene annotations | Cancer gene Fused withTSGene |
* 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 |
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TissGeneExp for CDH4 |
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 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 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. |
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) |
- 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 |
THCA | 3.126129442 | 0.057980289 | 3.068149153 | 7.65E-14 | 7.99E-13 |
BRCA | -1.161501275 | 1.068607497 | -2.230108772 | 2.79E-30 | 3.83E-29 |
KIRC | 3.165197921 | 0.286540977 | 2.878656944 | 6.99E-11 | 2.53E-10 |
HNSC | 1.270580447 | -0.1596056 | 1.430186047 | 0.00175 | 0.005514706 |
KICH | -0.938585135 | 0.489566865 | -1.428152 | 0.000991 | 0.002149768 |
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TissGene-miRNA for CDH4 |
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 CDH4 |
TissGeneSNV for CDH4 |
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. |
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) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.E403K | SKCM | 5 |
p.E329K | SKCM | 4 |
p.T414M | STAD | 2 |
p.V520M | STAD | 2 |
p.A612T | UCEC | 2 |
p.R817C | STAD | 2 |
p.E400K | SKCM | 2 |
p.K551R | COAD | 2 |
p.D894N | SKCM | 2 |
p.R349Q | SKCM | 2 |
p.D775N | LUAD | 1 |
p.N388S | HNSC | 1 |
p.K78N | ESCA | 1 |
p.P831S | SKCM | 1 |
p.R444H | UCEC | 1 |
p.G419R | SKCM | 1 |
p.P550T | LUAD | 1 |
p.V648I | STAD | 1 |
p.D644N | SKCM | 1 |
p.M330I | BLCA | 1 |
p.D863Y | SARC | 1 |
p.R515L | OV | 1 |
p.Y243C | STAD | 1 |
p.A566V | LGG | 1 |
p.A683V | PAAD | 1 |
p.W171* | SKCM | 1 |
p.I173M | LUSC | 1 |
p.R677C | LGG | 1 |
p.D387N | HNSC | 1 |
p.D343N | COAD | 1 |
p.V880I | UCEC | 1 |
p.V520M | UCEC | 1 |
p.H128Y | LUAD | 1 |
p.G657S | SKCM | 1 |
p.D820N | BLCA | 1 |
p.P521T | LUAD | 1 |
p.T342P | SKCM | 1 |
p.A344V | UCEC | 1 |
p.V443I | STAD | 1 |
p.R317W | PAAD | 1 |
p.W662C | LUSC | 1 |
p.P373S | SKCM | 1 |
p.L739F | SKCM | 1 |
p.L751M | UCEC | 1 |
p.E545K | SKCM | 1 |
p.E582K | BLCA | 1 |
p.P146L | ESCA | 1 |
p.A304T | SKCM | 1 |
p.R317Q | BLCA | 1 |
p.P437L | SKCM | 1 |
p.Y893H | THCA | 1 |
p.V456M | STAD | 1 |
p.P831T | LUAD | 1 |
p.G366E | LUSC | 1 |
p.A492V | ACC | 1 |
p.T634M | STAD | 1 |
p.R237L | LUAD | 1 |
p.G136E | SARC | 1 |
p.T876I | SKCM | 1 |
p.R204Q | LGG | 1 |
p.T471I | STAD | 1 |
p.I654S | READ | 1 |
p.R44Q | READ | 1 |
p.I265V | ACC | 1 |
p.P275S | ESCA | 1 |
p.D223N | BLCA | 1 |
p.R462Q | SKCM | 1 |
p.R194W | OV | 1 |
p.T101M | UCEC | 1 |
p.Q801K | LUAD | 1 |
p.E619K | SKCM | 1 |
p.S335N | COAD | 1 |
p.G731S | SKCM | 1 |
p.M754I | KIRP | 1 |
p.L413F | SKCM | 1 |
p.P144H | LUAD | 1 |
p.G399R | SKCM | 1 |
p.S195Y | BRCA | 1 |
p.T101M | BLCA | 1 |
p.G210S | SKCM | 1 |
p.G312E | SKCM | 1 |
p.A161G | LUAD | 1 |
p.V352A | SKCM | 1 |
p.E871K | SKCM | 1 |
p.E144K | SKCM | 1 |
p.P146S | SKCM | 1 |
p.G723D | UCEC | 1 |
p.P326Q | LUAD | 1 |
p.Q420E | SKCM | 1 |
p.D892E | HNSC | 1 |
p.S150F | SKCM | 1 |
p.A428T | LIHC | 1 |
p.T220I | COAD | 1 |
p.A301T | SKCM | 1 |
p.S224F | SKCM | 1 |
p.P757S | SKCM | 1 |
p.F318L | COAD | 1 |
p.D170N | SKCM | 1 |
p.M229V | BLCA | 1 |
p.T858K | LUAD | 1 |
p.R274G | ESCA | 1 |
p.A404V | COAD | 1 |
p.R666S | LUAD | 1 |
p.A87T | UCEC | 1 |
p.D820N | SKCM | 1 |
p.P187L | SKCM | 1 |
p.D39V | LUAD | 1 |
p.G804S | SKCM | 1 |
p.V525M | CESC | 1 |
p.P260L | DLBC | 1 |
p.P447S | SKCM | 1 |
p.A656V | UCEC | 1 |
p.E624K | GBM | 1 |
p.T576S | KIRC | 1 |
p.R130Q | COAD | 1 |
p.G493R | SKCM | 1 |
p.A428V | UCEC | 1 |
p.S873R | LUAD | 1 |
p.D262N | DLBC | 1 |
p.G610E | SKCM | 1 |
p.P82L | SKCM | 1 |
p.T309M | PRAD | 1 |
p.P823L | STAD | 1 |
p.T802I | SKCM | 1 |
p.R154W | COAD | 1 |
p.Y575C | STAD | 1 |
p.S126P | LIHC | 1 |
p.S545* | BLCA | 1 |
p.H808Y | UCEC | 1 |
p.D262H | HNSC | 1 |
p.E871G | PAAD | 1 |
p.R349* | STAD | 1 |
p.G163E | SKCM | 1 |
p.V776I | BLCA | 1 |
p.D718N | SKCM | 1 |
p.A241T | LGG | 1 |
p.V296M | PRAD | 1 |
p.R204W | BRCA | 1 |
p.L700V | LUAD | 1 |
p.L665F | SKCM | 1 |
p.P363L | SKCM | 1 |
p.A566V | ACC | 1 |
p.R204Q | SKCM | 1 |
p.G80W | LIHC | 1 |
p.V278A | SKCM | 1 |
p.G284S | SKCM | 1 |
p.P249S | SKCM | 1 |
p.E762K | SKCM | 1 |
p.V525M | PAAD | 1 |
p.A398V | UCEC | 1 |
p.R315W | CESC | 1 |
p.V816M | STAD | 1 |
p.P642S | SKCM | 1 |
p.T309K | LIHC | 1 |
p.G51V | BLCA | 1 |
p.V736M | BLCA | 1 |
p.E218K | SKCM | 1 |
p.E52G | UCEC | 1 |
p.P861S | SKCM | 1 |
p.P594L | STAD | 1 |
p.R315W | KIRC | 1 |
p.D96N | SKCM | 1 |
p.P156L | SKCM | 1 |
p.P828L | GBM | 1 |
p.F277L | KIRP | 1 |
p.D715E | BLCA | 1 |
p.G900R | SKCM | 1 |
p.V880I | UVM | 1 |
p.R315Q | PAAD | 1 |
p.P593L | STAD | 1 |
p.P133L | LUAD | 1 |
p.S224C | BLCA | 1 |
p.S886F | BLCA | 1 |
p.G89E | SKCM | 1 |
p.V448I | PRAD | 1 |
p.G163R | ACC | 1 |
p.V568M | SKCM | 1 |
p.D908E | HNSC | 1 |
p.V409M | PRAD | 1 |
p.R536Q | SKCM | 1 |
p.D610G | STAD | 1 |
p.E785A | BLCA | 1 |
p.E111K | SKCM | 1 |
p.A826T | LUSC | 1 |
p.Q802H | SARC | 1 |
p.G89R | ACC | 1 |
p.P323S | SKCM | 1 |
p.H131N | LUSC | 1 |
p.A115S | LUAD | 1 |
p.V286M | UCEC | 1 |
p.T35I | COAD | 1 |
p.R677C | STAD | 1 |
p.A227T | SKCM | 1 |
p.V409M | STAD | 1 |
p.P505S | HNSC | 1 |
p.E377K | SKCM | 1 |
p.G136R | SARC | 1 |
p.D384N | SKCM | 1 |
p.E180D | LUAD | 1 |
p.A778T | READ | 1 |
p.P187S | SKCM | 1 |
p.E326K | SKCM | 1 |
p.E451K | SKCM | 1 |
p.G684E | SKCM | 1 |
p.R228L | LUSC | 1 |
p.E29K | ACC | 1 |
p.L25V | BRCA | 1 |
p.P505L | HNSC | 1 |
p.E760Q | BLCA | 1 |
p.D820H | BLCA | 1 |
p.V359I | STAD | 1 |
p.V102M | SKCM | 1 |
p.A877T | ESCA | 1 |
p.V415M | SKCM | 1 |
p.D570E | KIRC | 1 |
p.A620S | THYM | 1 |
p.L153Q | LUAD | 1 |
p.N716K | UCEC | 1 |
p.F35L | SKCM | 1 |
p.A852S | HNSC | 1 |
p.V410I | SKCM | 1 |
p.S307I | LUAD | 1 |
p.G878S | SKCM | 1 |
p.N271K | LUAD | 1 |
p.A620V | STAD | 1 |
p.A167T | LGG | 1 |
p.K707N | PRAD | 1 |
p.P127L | LAML | 1 |
p.G889R | UCEC | 1 |
p.D306N | SKCM | 1 |
p.A378T | SKCM | 1 |
p.T307A | COAD | 1 |
p.R603C | LGG | 1 |
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TissGeneCNV for CDH4 |
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 CDH4 |
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 |
Chimerdb3.0 | FusionScan | BRCA | TCGA-E2-A1LL-01A | SS18L1-CDH4 | In-Frame | chr20:60718945 | chr20:60469965 |
Chimerdb3.0 | FusionScan | LUAD | TCGA-05-4244-01A | TOP1-CDH4 | In-Frame | chr20:39658095 | chr20:60318618 |
Chimerdb3.0 | TopHat-Fusion | BRCA | TCGA-E2-A1LL-01A | SS18L1-CDH4 | In-Frame | chr20:60718944 | chr20:60469965 |
TCGAfusionPortal | PRADA | BLCA | TCGA-GC-A3RB-01A | OSBPL2-CDH4 | 5UTR-CDS | Chr20:60813653 | Chr20:60485478 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A1-A0SJ-01A | ZFC3H1-CDH4 | Out-of-frame | Chr12:72013095 | Chr20:60427810 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A7-A13F-01A | TAF4-CDH4 | Out-of-frame | Chr20:60639507 | Chr20:59829882 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A8-A091-01A | NCOA5-CDH4 | Out-of-frame | Chr20:44708026 | Chr20:60318619 |
TCGAfusionPortal | PRADA | BRCA | TCGA-AC-A62V-01A | CDH4-SLA2 | Out-of-frame | Chr20:60448956 | Chr20:35262992 |
TCGAfusionPortal | PRADA | BRCA | TCGA-E2-A1LL-01A | SS18L1-CDH4 | In-frame | Chr20:60718945 | Chr20:60469966 |
TCGAfusionPortal | PRADA | BRCA | TCGA-EW-A1PA-01A | CDH4-NLRP9 | Out-of-frame | Chr20:60348238 | Chr19:56244916 |
TCGAfusionPortal | PRADA | LUAD | TCGA-05-4244-01A | TOP1-CDH4 | In-frame | Chr20:39658095 | Chr20:60318619 |
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TissGeneNet for CDH4 |
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) |
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TissGeneProg for CDH4 |
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. |
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. |
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. |
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 CDH4 |
TissGeneDrug for CDH4 |
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 CDH4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0009402 | Colorectal Carcinoma | 1 | BeFree |
umls:C0017185 | Gastrointestinal Neoplasms | 1 | BeFree |
umls:C0022658 | Kidney Diseases | 1 | GAD |
umls:C0024623 | Malignant neoplasm of stomach | 1 | BeFree |
umls:C0028754 | Obesity | 1 | GWASCAT |
umls:C0038454 | Cerebrovascular accident | 1 | GAD |
umls:C0038525 | Subarachnoid Hemorrhage | 1 | GAD |
umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
umls:C0151699 | Intracranial Hemorrhages | 1 | GAD |
umls:C0596263 | Carcinogenesis | 1 | BeFree |
umls:C0699791 | Stomach Carcinoma | 1 | BeFree |
umls:C1527249 | Colorectal Cancer | 1 | BeFree |
umls:C2931822 | Nasopharyngeal carcinoma | 1 | BeFree |
umls:C2937358 | Cerebral Hemorrhage | 1 | GAD |