TissGDB

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

TissGeneSummary for RTKN2

Gene summary

Basic gene information	Gene symbol	RTKN2
	Gene name	rhotekin 2
	Synonyms	PLEKHK1\|bA531F24.1
	Cytomap	UCSC genome browser: 10q21.2
	Type of gene	protein-coding
	RefGenes	NM_001282941.1, NM_145307.3,
	Description	PH domain-containing family K member 1pleckstrin homology domain containing, family K member 1pleckstrin homology domain-containing family K member 1rhotekin-2
	Modification date	20141211
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000182010
	HPRD : 17863
	Vega : OTTHUMG00000018299
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RTKN2
	BioGPS: 219790
Pathway	NCI Pathway Interaction Database: RTKN2
	KEGG: RTKN2
	REACTOME: RTKN2
	Pathway Commons: RTKN2
Context	iHOP: RTKN2
	ligand binding site mutation search in PubMed: RTKN2
	UCL Cancer Institute: RTKN2
Assigned class in TissGDB*	C
Included tissue-specific gene expression resources	HPA,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)	Lung
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	LUAD,LUSC
Reference showing the relevant tissue of RTKN2
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

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TissGeneExp for RTKN2

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
LIHC	-3.169050983	-5.147532983	1.978482	7.73E-09	6.89E-08
BRCA	-0.016151685	-1.99503765	1.978885965	2.77E-34	4.96E-33
PRAD	-0.649555599	-1.679782522	1.030226923	6.00E-07	4.48E-06
KICH	-4.111908983	-2.721220983	-1.390688	1.07E-05	3.38E-05
LUAD	0.335782465	4.988235913	-4.652453448	1.58E-43	1.77E-40
LUSC	0.383273134	4.628275095	-4.245001961	1.60E-32	1.09E-30
BLCA	0.393426385	-2.050778878	2.444205263	0.000367	0.003151382
STAD	0.477204017	-1.718595983	2.1958	1.94E-05	0.000199226

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TissGene-miRNA for RTKN2

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
UCS	hsa-miR-103a-3p	MIMAT0000101	0.045	-0.27	56
UCS	hsa-miR-30a-5p	MIMAT0000087	0.04	-0.28	56

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TissGeneMut for RTKN2

TissGeneSNV for RTKN2

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.A328V	KIRC	3
p.E327K	TGCT	3
p.R33*	UCEC	3
p.R33*	SKCM	2
p.L213I	TGCT	1
p.R33X	SKCM	1
p.K93E	PAAD	1
p.A246D	ESCA	1
p.W39*	SKCM	1
p.R127C	UCEC	1
p.F457L	UCEC	1
p.W530C	LUAD	1
p.R33X	COAD	1
p.E36K	CESC	1
p.R414Q	PRAD	1
p.G100V	READ	1
p.R33Q	HNSC	1
p.R126G	UCEC	1
p.R33X	READ	1
p.K352R	HNSC	1
p.I152N	KIRC	1
p.P505L	SKCM	1
p.R108*	UCEC	1
p.G37R	LIHC	1
p.L58F	UCEC	1
p.H400Y	COAD	1
p.D350E	BRCA	1
p.K383N	STAD	1
p.M556V	LGG	1
p.F526L	CESC	1
p.D117H	BRCA	1
p.C221X	ESCA	1
p.H551D	LUAD	1
p.W39X	SKCM	1
p.S70T	COAD	1
p.E286K	BLCA	1
p.E327K	KICH	1
p.A471P	LIHC	1
p.W604C	GBM	1
p.K399N	LUSC	1
p.A237S	LUSC	1
p.M347I	LUAD	1
p.T522K	PAAD	1
p.T181I	UCS	1
p.M411K	SKCM	1
p.R276P	BLCA	1
p.R591S	LIHC	1
p.K544E	UCEC	1
p.D49N	UCS	1
p.E182D	COAD	1
p.R108Q	COAD	1
p.S200Y	THYM	1
p.E574K	BLCA	1
p.A328V	TGCT	1
p.E327K	KIRP	1
p.D496A	KIRC	1
p.K251N	HNSC	1
p.S534C	LIHC	1
p.L541S	COAD	1
p.K596N	COAD	1
p.H253P	MESO	1
p.E327K	THYM	1
p.S116F	HNSC	1
p.S70L	SKCM	1
p.D115G	SKCM	1

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TissGeneCNV for RTKN2

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 RTKN2

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	ChiTaRs	NA	BF853289	RTKN2-KIAA0100		chr10:63986787	chr17:26966177
Chimerdb3.0	FusionScan	ESCA	TCGA-R6-A6Y2-01B	MALT1-RTKN2	In-Frame	chr18:56367823	chr10:63959620
Chimerdb3.0	FusionScan	ESCA	TCGA-L5-A8NR-01A	REEP3-RTKN2	Out-of-Frame	chr10:65359043	chr10:64005816
TCGAfusionPortal	PRADA	BRCA	TCGA-A2-A25B-01A	KAT6B-RTKN2	In-frame	Chr10:76785007	Chr10:64000954
TCGAfusionPortal	PRADA	PRAD	TCGA-J4-A83I-01A	KCNMB4-RTKN2	Out-of-frame	Chr12:70760850	Chr10:63996022
TCGAfusionPortal	PRADA	PRAD	TCGA-J4-A83I-01A	ADAMTS17-RTKN2	In-frame	Chr15:100537590	Chr10:64022580

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TissGeneNet for RTKN2

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)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

COAD (tumor)	COAD (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

HNSC (tumor)	HNSC (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

KICH (tumor)	KICH (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

KIRC (tumor)	KIRC (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

KIRP (tumor)	KIRP (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

LIHC (tumor)	LIHC (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

LUAD (tumor)	LUAD (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

LUSC (tumor)	LUSC (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

PRAD (tumor)	PRAD (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

STAD (tumor)	STAD (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

THCA (tumor)	THCA (normal)
RTKN2, PACSIN1 (tumor)	RTKN2, PACSIN1 (normal)

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TissGeneProg for RTKN2

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 RTKN2

TissGeneDrug for RTKN2

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 RTKN2

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

Disease ID	Disease name	# pubmeds	Source
umls:C0003873	Rheumatoid Arthritis	1	BeFree,GWASCAT
umls:C0036341	Schizophrenia	1	BeFree