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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 CDH16
check button Gene summary
Basic gene informationGene symbolCDH16
Gene namecadherin 16, KSP-cadherin
Synonyms-
CytomapUCSC genome browser: 16q22.1
Type of geneprotein-coding
RefGenesNM_001204744.1,
NM_001204745.1,NM_001204746.1,NM_004062.3,
DescriptionKSP-cadherincadherin-16kidney-specific cadherin
Modification date20141207
dbXrefs MIM : 603118
HGNC : HGNC
Ensembl : ENSG00000166589
HPRD : 11929
Vega : OTTHUMG00000137518
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CDH16
BioGPS: 1014
PathwayNCI Pathway Interaction Database: CDH16
KEGG: CDH16
REACTOME: CDH16
Pathway Commons: CDH16
ContextiHOP: CDH16
ligand binding site mutation search in PubMed: CDH16
UCL Cancer Institute: CDH16
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,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 CDH16
Description by TissGene annotationsProtective TissGene in OS
Protective TissGene in RFS
TissgsKTS
CNV gained TissGeneKTS
* 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


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TissGeneExp for CDH16

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
KIRP7.75564390610.10535016-2.349706257.03E-118.47E-10
LUAD-3.817153292-1.920672258-1.8964810344.16E-154.30E-14
THCA0.7867510046.533856088-5.7471050853.48E-232.49E-21
KIRC7.2307959899.897962656-2.6671666678.27E-311.72E-29
KICH8.02673615610.01022016-1.9834840.00230.004672074
PRAD-4.498372921-3.357392152-1.1409807690.0004930.001742607


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TissGene-miRNA for CDH16

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 CDH16
TissGeneSNV for CDH16

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.R164*STAD2
p.E480KSKCM2
p.E436KSKCM2
p.E383KSKCM2
p.R164XSTAD2
p.E339KSKCM2
p.R484HUCEC1
p.P574LSKCM1
p.R311XACC1
p.P644RBLCA1
p.P124TGBM1
p.E88KBLCA1
p.E281DOV1
p.R679HACC1
p.T619ISKCM1
p.A317VPRAD1
p.A317VBLCA1
p.R86QHNSC1
p.G189ESKCM1
p.V56MLGG1
p.R242CSKCM1
p.A489VGBM1
p.A64TCOAD1
p.E87XSTAD1
p.G447SSKCM1
p.H682YDLBC1
p.G508ELGG1
p.A446TSTAD1
p.I234TSTAD1
p.V712LLUSC1
p.L348FSTAD1
p.G195ESKCM1
p.L203PBLCA1
p.P591LSKCM1
p.E28KHNSC1
p.G313SSKCM1
p.D340NHNSC1
p.R408*ACC1
p.D462NSKCM1
p.G35ESKCM1
p.D231NSKCM1
p.D328NSKCM1
p.Y577XSKCM1
p.E521KSKCM1
p.V795ISKCM1
p.D821NBLCA1
p.A489VPRAD1
p.E149QBLCA1
p.S452FSKCM1
p.G216DSKCM1
p.K814EKICH1
p.P141HUCEC1
p.R153QLUAD1
p.E616KSKCM1
p.V698ISKCM1
p.L207ICOAD1
p.V573AUCEC1
p.R484CSTAD1
p.R717CBLCA1
p.P38SSKCM1
p.T729NLUSC1
p.P109SLGG1
p.A51TTHCA1
p.P351LLUSC1
p.P562TLUAD1
p.F147LBLCA1
p.G313DSKCM1
p.R140KSKCM1
p.Y674*UCEC1
p.D331EBLCA1
p.P460LSKCM1
p.D815NSKCM1
p.S355FSKCM1
p.V529GLGG1
p.P671LSKCM1
p.P38HSKCM1
p.E436KPRAD1
p.R594QLAML1
p.Q533HBLCA1
p.I442TSTAD1
p.R86QSKCM1
p.D543NSKCM1
p.E119DUCEC1
p.I442FBLCA1
p.Y674*SKCM1
p.P45LLUAD1
p.E87*STAD1
p.P816SBLCA1
p.D215NSKCM1
p.E434*BRCA1
p.E339XCOAD1
p.D347YREAD1
p.L646MESCA1
p.G544SSKCM1
p.A425TSTAD1
p.E250DCOAD1
p.R776CSTAD1
p.E519KSKCM1
p.A225TSKCM1
p.E424KSKCM1
p.P30SSKCM1
p.R339CSKCM1
p.D718NSKCM1
p.T226ISTAD1
p.P562LHNSC1
p.G216SSKCM1
p.P494LSKCM1
p.L163FSARC1
p.E293QBRCA1
p.R164QLUAD1
p.S458RUCEC1
p.R679HTHYM1
p.D640NSKCM1
p.E155KSKCM1
p.L41QLUAD1
p.E616KHNSC1
p.G286ESKCM1
p.R48CLUSC1
p.E329DUCEC1
p.N120KLUAD1
p.P319HUCEC1
p.V558MSTAD1
p.T666SUCS1
p.P395ROV1
p.R408XACC1
p.A128TSKCM1
p.A620THNSC1
p.T467SLUAD1
p.H275NUCEC1
p.P465HLUSC1
p.V276IREAD1


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TissGeneCNV for CDH16

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 CDH16

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 CDH16

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)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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COAD (tumor)COAD (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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HNSC (tumor)HNSC (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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KICH (tumor)KICH (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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KIRC (tumor)KIRC (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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KIRP (tumor)KIRP (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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LIHC (tumor)LIHC (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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LUAD (tumor)LUAD (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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LUSC (tumor)LUSC (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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PRAD (tumor)PRAD (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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STAD (tumor)STAD (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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THCA (tumor)THCA (normal)
CDH16, CTNNB1, EGR1, G6PC (tumor)CDH16, CTNNB1, EGR1, G6PC (normal)
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TissGeneProg for CDH16

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 CDH16
TissGeneDrug for CDH16

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 CDH16

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0007134Renal Cell Carcinoma2BeFree,LHGDN
umls:C0549473Thyroid carcinoma2BeFree
umls:C1510502Oxyphilic Adenoma2BeFree,LHGDN
umls:C0022665Kidney Neoplasm1BeFree
umls:C0027660Neoplasms, Glandular and Epithelial1LHGDN
umls:C0220615Adult Acute Myeloblastic Leukemia1BeFree
umls:C0346255Oncocytoma, renal1BeFree
umls:C0949541Hurthle Cell Tumor1BeFree
umls:C1266042Chromophobe Renal Cell Carcinoma1BeFree
umls:C1378050Oncocytic Neoplasm1BeFree