TissGDB

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	TissGeneSummary
	TissGeneExp
	TissGene-miRNA
	TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions
	TissGeneNet
	TissGeneProg
	TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for NEK2

Gene summary

Basic gene information	Gene symbol	NEK2
	Gene name	NIMA-related kinase 2
	Synonyms	HsPK21\|NEK2A\|NLK1\|PPP1R111\|RP67
	Cytomap	UCSC genome browser: 1q32.3
	Type of gene	protein-coding
	RefGenes	NM_001204182.1, NM_001204183.1,NM_002497.3,
	Description	NIMA (never in mitosis gene a)-related kinase 2nimA-like protein kinase 1nimA-related protein kinase 2protein phosphatase 1, regulatory subunit 111serine/threonine-protein kinase Nek2
	Modification date	20141222
dbXrefs	MIM : 604043
	HGNC : HGNC
	Ensembl : ENSG00000117650
	HPRD : 04953
	Vega : OTTHUMG00000037121
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NEK2
	BioGPS: 4751
Pathway	NCI Pathway Interaction Database: NEK2
	KEGG: NEK2
	REACTOME: NEK2
	Pathway Commons: NEK2
Context	iHOP: NEK2
	ligand binding site mutation search in PubMed: NEK2
	UCL Cancer Institute: NEK2
Assigned class in TissGDB*	B
Included tissue-specific gene expression resources	HPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)	BladderTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	BLCATGCT
Reference showing the relevant tissue of NEK2
Description by TissGene annotations	Cancer gene

* 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:0006468	protein phosphorylation	21076410
GO:0007059	chromosome segregation	14978040
GO:0046777	protein autophosphorylation	17626005
GO:0051299	centrosome separation	18086858
GO:0006468	protein phosphorylation	21076410
GO:0007059	chromosome segregation	14978040
GO:0046777	protein autophosphorylation	17626005
GO:0051299	centrosome separation	18086858

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TissGeneExp for NEK2

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
PRAD	-1.948627357	-3.694986973	1.746359615	5.20E-10	9.10E-09
KIRC	-1.51805834	-4.020465285	2.502406944	7.03E-24	7.57E-23
BLCA	1.94783742	-2.079436264	4.027273684	2.79E-06	7.39E-05
KIRP	-2.020898271	-4.607504521	2.58660625	9.71E-08	5.85E-07
BRCA	1.808729525	-2.747202931	4.555932456	5.06E-64	5.70E-61
STAD	1.698379854	-1.215563896	2.91394375	2.12E-07	4.92E-06
COAD	2.291461104	0.776703412	1.514757692	2.40E-11	4.21E-10
LUSC	1.990785614	-2.780947719	4.771733333	3.20E-40	3.60E-37
LIHC	0.148849104	-3.780906896	3.929756	3.47E-21	2.41E-19
HNSC	1.711836686	-0.148800524	1.860637209	1.17E-09	1.85E-08
LUAD	1.035564552	-2.62899062	3.664555172	1.72E-28	1.24E-26
KICH	-2.944748896	-4.337996896	1.393248	0.00243	0.004891068
ESCA	1.645711104	-2.180161623	3.825872727	4.09E-05	0.001716257

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TissGene-miRNA for NEK2

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 NEK2

TissGeneSNV for NEK2

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.A123V	SKCM	2
p.S296L	UCEC	2
p.N350H	BLCA	1
p.Q329X	STAD	1
p.S402G	KIRC	1
p.E223K	UCEC	1
p.L224V	HNSC	1
p.E38Q	CESC	1
p.G388E	LUAD	1
p.T179K	THYM	1
p.E360K	SKCM	1
p.N433K	UCEC	1
p.T249M	STAD	1
p.T170M	ACC	1
p.L202W	BLCA	1
p.G388R	GBM	1
p.H258Y	SKCM	1
p.E104D	UCEC	1
p.L320P	SKCM	1
p.Y41H	ESCA	1
p.G92V	UCEC	1
p.R280K	BLCA	1
p.R140W	STAD	1
p.R239G	KIRP	1
p.Q312*	SKCM	1
p.R69C	UCS	1
p.P293R	LIHC	1
p.D7E	LIHC	1
p.R288*	UCEC	1
p.R337C	HNSC	1
p.S296L	SKCM	1
p.G158X	KIRP	1
p.L283V	BLCA	1
p.P237S	SKCM	1
p.G443C	UCEC	1
p.R115Q	UCEC	1
p.R259Q	MESO	1
p.Q329*	UCEC	1
p.S131N	SKCM	1
p.Y12C	BRCA	1

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TissGeneCNV for NEK2

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 NEK2

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	CESC	TCGA-DR-A0ZL-01A	NEK2-METTL13	In-Frame	chr1:211840447	chr1:171761156
Chimerdb3.0	FusionScan	BRCA	TCGA-A8-A09Q-01A	NVL-NEK2	In-Frame	chr1:224437913	chr1:211847855
TCGAfusionPortal	PRADA	BRCA	TCGA-A8-A09Q-01A	NVL-NEK2	In-frame	Chr1:224437914	Chr1:211847855

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TissGeneNet for NEK2

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)
NEK2, PPP1CC, PPP1CA, CTNNB1, PDE4DIP, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, CEP250, MAD1L1, NEK11, SPTBN4, RHOB, CCDC85A, CLEC4C, CHGA, C10orf137, IFT140 (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, MAPK1, PDE4DIP, MCC, NDC80, GIT1, CDC27, IMMT, DCTN1, TPM3, CEP250, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, C10orf137, IFT140 (normal)

COAD (tumor)	COAD (normal)
NEK2, PPP1CC, PPP1CA, MAPK1, CTNNB1, PDE4DIP, MCC, NDC80, IMMT, DCTN1, TPM3, CDC26, CEP250, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, PPP1R2, CHGA (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, CTNNB1, MCC, NDC80, CDC27, IMMT, DCTN1, TPM3, CDC26, CEP250, MAD1L1, NEK11, SPTBN4, RHOB, CCDC85A, CHGA, C10orf137, IFT140 (normal)

HNSC (tumor)	HNSC (normal)
NEK2, PPP1CC, PPP1CA, TCF25, MAPK1, PDE4DIP, MCC, NDC80, GIT1, CDC16, IMMT, DCTN1, TPM3, CEP250, MAD1L1, SPTBN4, EIF4A2, RHOB, CCDC85A, PPP1R2, C10orf137 (tumor)	NEK2, PPP1CC, TCF25, MCC, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, CDC26, CEP250, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, PPP1R2, C10orf137, IFT140 (normal)

KICH (tumor)	KICH (normal)
NEK2, PPP1CC, PPP1CA, TCF25, MAPK1, CTNNB1, PDE4DIP, MCC, NDC80, GIT1, CDC16, CDC27, IMMT, TPM3, CDC26, CEP250, MAD1L1, NEK11, SPTBN4, RHOB, CLEC4C (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, CTNNB1, PDE4DIP, MCC, NDC80, CDC16, CDC27, TPM3, CDC26, CEP250, MAD1L1, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, CHGA, C10orf137 (normal)

KIRC (tumor)	KIRC (normal)
NEK2, PPP1CC, MAPK1, CTNNB1, PDE4DIP, NDC80, GIT1, CDC16, CDC27, IMMT, TPM3, CDC26, CEP250, MAD1L1, SPTBN4, EIF4A2, RHOB, CLEC4C, PPP1R2, C10orf137, IFT140 (tumor)	NEK2, PPP1CC, TCF25, CTNNB1, PDE4DIP, MCC, NDC80, GIT1, CDC27, DCTN1, TPM3, CEP250, MAD1L1, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, CHGA, C10orf137 (normal)

KIRP (tumor)	KIRP (normal)
NEK2, MAPK1, CTNNB1, PDE4DIP, NDC80, GIT1, CDC16, CDC27, IMMT, TPM3, CDC26, CEP250, MAD1L1, NEK11, SPTBN4, RHOB, CCDC85A, CLEC4C, PPP1R2, C10orf137, IFT140 (tumor)	NEK2, PPP1CC, TCF25, CTNNB1, PDE4DIP, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, TPM3, CDC26, CEP250, MAD1L1, NEK11, EIF4A2, RHOB, CHGA, C10orf137, IFT140 (normal)

LIHC (tumor)	LIHC (normal)
NEK2, PPP1CC, PPP1CA, TCF25, MCC, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, TPM3, MAD1L1, NEK11, SPTBN4, RHOB, CCDC85A, PPP1R2, CHGA, C10orf137, IFT140 (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, MAPK1, CTNNB1, MCC, NDC80, GIT1, CDC27, DCTN1, TPM3, CDC26, CEP250, SPTBN4, EIF4A2, RHOB, CCDC85A, PPP1R2, CHGA, C10orf137 (normal)

LUAD (tumor)	LUAD (normal)
NEK2, PPP1CC, PPP1CA, TCF25, MAPK1, MCC, NDC80, GIT1, CDC16, DCTN1, TPM3, CDC26, MAD1L1, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, PPP1R2, CHGA, C10orf137 (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, PDE4DIP, MCC, NDC80, GIT1, CDC27, IMMT, DCTN1, TPM3, CDC26, CEP250, NEK11, SPTBN4, RHOB, CCDC85A, PPP1R2, CHGA, IFT140 (normal)

LUSC (tumor)	LUSC (normal)
NEK2, PPP1CC, PPP1CA, TCF25, CTNNB1, PDE4DIP, MCC, NDC80, CDC16, IMMT, TPM3, CDC26, CEP250, MAD1L1, NEK11, SPTBN4, RHOB, CCDC85A, CLEC4C, CHGA, C10orf137 (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, MCC, NDC80, GIT1, CDC27, IMMT, DCTN1, TPM3, CDC26, MAD1L1, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, PPP1R2, C10orf137, IFT140 (normal)

PRAD (tumor)	PRAD (normal)
NEK2, PPP1CC, TCF25, PDE4DIP, MCC, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, TPM3, CEP250, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, CHGA, C10orf137, IFT140 (tumor)	NEK2, PPP1CC, TCF25, CTNNB1, PDE4DIP, MCC, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, TPM3, CDC26, CEP250, NEK11, SPTBN4, RHOB, CCDC85A, CHGA, C10orf137 (normal)

STAD (tumor)	STAD (normal)
NEK2, PPP1CA, MAPK1, PDE4DIP, MCC, NDC80, GIT1, CDC16, CDC27, DCTN1, TPM3, CEP250, MAD1L1, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, PPP1R2, C10orf137, IFT140 (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, CTNNB1, PDE4DIP, MCC, NDC80, GIT1, CDC16, CDC27, IMMT, DCTN1, TPM3, CEP250, SPTBN4, RHOB, CCDC85A, CLEC4C, CHGA, IFT140 (normal)

THCA (tumor)	THCA (normal)
NEK2, PPP1CC, PPP1CA, MAPK1, CTNNB1, PDE4DIP, NDC80, IMMT, DCTN1, TPM3, CDC26, CEP250, MAD1L1, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, PPP1R2, IFT140 (tumor)	NEK2, PPP1CC, PPP1CA, TCF25, MAPK1, CTNNB1, PDE4DIP, NDC80, CDC27, TPM3, CEP250, MAD1L1, NEK11, SPTBN4, EIF4A2, RHOB, CCDC85A, CLEC4C, PPP1R2, C10orf137, IFT140 (normal)

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TissGeneProg for NEK2

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 NEK2

TissGeneDrug for NEK2

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 NEK2

Disease information associated with TissGene
(DisGeNet, 2016-06-01)

Disease ID	Disease name	# pubmeds	Source
umls:C0006142	Malignant neoplasm of breast	13	BeFree,GAD
umls:C0678222	Breast Carcinoma	11	BeFree
umls:C0079744	Diffuse Large B-Cell Lymphoma	3	BeFree
umls:C0206698	Cholangiocarcinoma	3	BeFree
umls:C0009402	Colorectal Carcinoma	2	BeFree
umls:C0026764	Multiple Myeloma	2	BeFree
umls:C0029925	Ovarian Carcinoma	2	BeFree
umls:C0152013	Adenocarcinoma of lung (disorder)	2	BeFree
umls:C0235974	Pancreatic carcinoma	2	BeFree
umls:C0346647	Malignant neoplasm of pancreas	2	BeFree
umls:C0596263	Carcinogenesis	2	BeFree
umls:C1140680	Malignant neoplasm of ovary	2	BeFree
umls:C1527249	Colorectal Cancer	2	BeFree
umls:C3539878	Triple Negative Breast Neoplasms	2	BeFree
umls:C0007124	Noninfiltrating Intraductal Carcinoma	1	BeFree
umls:C0007131	Non-Small Cell Lung Carcinoma	1	BeFree
umls:C0019693	HIV Infections	1	BeFree
umls:C0027627	Neoplasm Metastasis	1	BeFree
umls:C0036631	Seminoma	1	BeFree
umls:C0178874	Tumor Progression	1	BeFree
umls:C0341439	Chronic liver disease	1	BeFree
umls:C0597984	Biliary stricture	1	BeFree
umls:C0750952	Biliary Tract Cancer	1	BeFree
umls:C1134719	Invasive Ductal Breast Carcinoma	1	BeFree
umls:C1176475	Ductal Carcinoma	1	BeFree,LHGDN
umls:C1449563	Cardiomyopathy, Familial Idiopathic	1	BeFree
umls:C2239176	Liver carcinoma	1	BeFree
umls:C0035334	Retinitis Pigmentosa	0	ORPHANET
umls:C3809954	RETINITIS PIGMENTOSA 67	0	CLINVAR