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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 CCDC65
check button Gene summary
Basic gene informationGene symbolCCDC65
Gene namecoiled-coil domain containing 65
SynonymsCILD27|FAP250|NYD-SP28
CytomapUCSC genome browser: 12q13.12
Type of geneprotein-coding
RefGenesNM_001286957.1,
NM_033124.4,
Descriptioncoiled-coil domain-containing protein 65testis development protein NYD-SP28
Modification date20141207
dbXrefs MIM : 611088
HGNC : HGNC
Ensembl : ENSG00000139537
HPRD : 14867
Vega : OTTHUMG00000170401
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCDC65
BioGPS: 85478
PathwayNCI Pathway Interaction Database: CCDC65
KEGG: CCDC65
REACTOME: CCDC65
Pathway Commons: CCDC65
ContextiHOP: CCDC65
ligand binding site mutation search in PubMed: CCDC65
UCL Cancer Institute: CCDC65
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)Testis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)TGCT
Reference showing the relevant tissue of CCDC65
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


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TissGeneExp for CCDC65

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
LUSC-0.1826707563.082560616-3.2652313731.41E-159.48E-15
KIRC1.6696891292.709291907-1.0396027781.60E-105.51E-10
LUAD0.7651494263.15149253-2.3863431035.62E-103.07E-09
KICH-0.4112778152.636378185-3.0476561.13E-142.09E-13
THCA1.7655025243.165221168-1.3997186441.14E-141.36E-13


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TissGene-miRNA for CCDC65

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 CCDC65
TissGeneSNV for CCDC65

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.
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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.R90*STAD1
p.I443MBLCA1
p.S185YREAD1
p.S283RLIHC1
p.K297NLGG1
p.R311KSKCM1
p.Q462ELUAD1
p.N409SPRAD1
p.M1VSTAD1
p.E257DBLCA1
p.K278NHNSC1
p.R305XCOAD1
p.K6NPAAD1
p.R315GLUAD1
p.K320NCOAD1
p.H475LLUAD1
p.E154KBLCA1
p.H475NLUAD1
p.E108KSKCM1
p.R70WLGG1
p.Y292CUCEC1
p.E82DESCA1
p.F42LREAD1
p.E71KSKCM1
p.H475ILUAD1
p.H133RCOAD1
p.E152KLUSC1
p.D478NUCS1
p.I183MDLBC1
p.R472HCOAD1
p.H169NCOAD1
p.P482AOV1
p.Y408CCOAD1
p.E359XESCA1
p.E359KSKCM1
p.N143KSARC1
p.E5*UCEC1
p.E76*STAD1
p.S101YUCEC1
p.R294HSTAD1
p.R90XSTAD1
p.N217DREAD1
p.F42LUCEC1
p.E448KSKCM1
p.E257QBLCA1
p.E76XSTAD1
p.R294CCOAD1
p.E448KUCEC1


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TissGeneCNV for CCDC65

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 CCDC65

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 CCDC65

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)


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TissGeneProg for CCDC65

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 CCDC65
TissGeneDrug for CCDC65

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 CCDC65

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0008780Ciliary Motility Disorders2BeFree
umls:C0022521Kartagener Syndrome2BeFree,CLINVAR
umls:C3809701CILIARY DYSKINESIA, PRIMARY, 270CLINVAR