TissGDB

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

TissGeneSummary for YBX2

Gene summary

Basic gene information	Gene symbol	YBX2
	Gene name	Y box binding protein 2
	Synonyms	CONTRIN\|CSDA3\|DBPC\|MSY2
	Cytomap	UCSC genome browser: 17p13.1
	Type of gene	protein-coding
	RefGenes	NM_015982.3,
	Description	DNA-binding protein CMSY2 homologY-box-binding protein 2germ cell specific Y-box binding proteingerm cell-specific Y-box-binding protein
	Modification date	20141207
dbXrefs	MIM : 611447
	HGNC : HGNC
	Ensembl : ENSG00000006047
	HPRD : 18311
	Vega : OTTHUMG00000177992
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_YBX2
	BioGPS: 51087
Pathway	NCI Pathway Interaction Database: YBX2
	KEGG: YBX2
	REACTOME: YBX2
	Pathway Commons: YBX2
Context	iHOP: YBX2
	ligand binding site mutation search in PubMed: YBX2
	UCL Cancer Institute: YBX2
Assigned class in TissGDB*	A
Included tissue-specific gene expression resources	HPA,TiGER,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 YBX2	Expression of Y-box-binding protein dbpC/contrin, a potentially new cancer/testis antigen. Br J Cancer. 2006 Mar 13;94(5):710-6. (pmid:16479255) go to article
Description by TissGene annotations	Have significant anti-correlated miRNA

* 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 YBX2

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
LUSC	-0.647385607	-3.538705214	2.891319608	8.39E-14	4.40E-13
LUAD	-0.271382598	-3.491477425	3.220094828	3.76E-13	3.07E-12
PRAD	-1.693319468	-0.491698314	-1.201621154	1.73E-06	1.17E-05
STAD	2.063756734	0.732141109	1.331615625	0.0134	0.043362014
HNSC	-1.588044065	-0.12094174	-1.467102326	0.00124	0.004078947
KICH	2.116373609	-0.049938391	2.166312	0.000217	0.000532

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TissGene-miRNA for YBX2

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
ACC	hsa-miR-3064-5p	MIMAT0019864	0.016	-0.28	78
ACC	hsa-miR-3064-5p	MIMAT0019864	0.016	-0.28	78
LUAD	hsa-let-7i-5p	MIMAT0000415	0.035	-0.28	60
ACC	hsa-miR-330-5p	MIMAT0004693	0.0074	-0.3	78
ACC	hsa-miR-330-5p	MIMAT0004693	0.0074	-0.3	78
LUAD	hsa-let-7b-5p	MIMAT0000063	0.0028	-0.38	60
LUAD	hsa-let-7f-5p	MIMAT0000067	0.00022	-0.46	60
LUAD	hsa-let-7a-5p	MIMAT0000062	0.000011	-0.54	60

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TissGeneMut for YBX2

TissGeneSNV for YBX2

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.S63P	SKCM	3
p.R233W	THCA	2
p.P188S	SKCM	2
p.G9V	PRAD	1
p.Q123*	SKCM	1
p.R182Q	LGG	1
p.Q123X	SKCM	1
p.T359N	KIRC	1
p.Q326*	HNSC	1
p.R318H	UCS	1
p.P352T	PRAD	1
p.S63P	KIRP	1
p.R320Q	SKCM	1
p.G164W	UCEC	1
p.R239Q	UCEC	1
p.R239W	HNSC	1
p.S63P	LGG	1
p.R286S	UCEC	1
p.T361P	LGG	1
p.G263R	SKCM	1
p.R181C	THCA	1
p.P175S	ESCA	1
p.S137C	LUAD	1
p.P226S	SKCM	1
p.A155T	READ	1
p.R178C	BLCA	1
p.E152D	UCEC	1
p.R290H	UCEC	1
p.S63P	PRAD	1
p.P188L	SKCM	1
p.R212W	LUSC	1
p.R221Q	UCEC	1
p.R271*	UCEC	1
p.V138A	GBM	1
p.R181C	SKCM	1
p.P238S	SKCM	1
p.R342W	HNSC	1
p.Q123H	PAAD	1
p.G268V	KIRP	1
p.R177Q	LIHC	1
p.P238S	ESCA	1

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TissGeneCNV for YBX2

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 YBX2

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	CA336584	PSMD2-YBX2		chr3:184017189	chr17:7191584

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TissGeneNet for YBX2

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 YBX2

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 YBX2

TissGeneDrug for YBX2

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 YBX2

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

Disease ID	Disease name	# pubmeds	Source
umls:C0004509	Azoospermia	2	BeFree,GAD
umls:C0021364	Male infertility	2	BeFree,GAD
umls:C0013377	Dysgerminoma	1	LHGDN
umls:C0028960	Oligospermia	1	GAD
umls:C0036631	Seminoma	1	LHGDN
umls:C0520933	Abnormal spermatogenesis	1	BeFree