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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: YBX1 (NCBI Gene ID:4904)

Gene Summary

Gene Summary

Gene Information	Gene Name: YBX1
	Gene ID: 4904
	Gene Symbol	YBX1
	Gene ID	4904
	Gene Name	Y-box binding protein 1
	Synonyms	BP-8\|CBF-A\|CSDA2\|CSDB\|DBPB\|EFI-A\|MDR-NF1\|NSEP-1\|NSEP1\|YB-1\|YB1
	Cytomap	1p34.2
	Type of Gene	protein-coding
	Description	Y-box-binding protein 1CCAAT-binding transcription factor I subunit ADNA-binding protein BY-box transcription factorenhancer factor I subunit Amajor histocompatibility complex, class II, Y box-binding protein Inuclease-sensitive element-binding prot
	Modification date	20200327
	UniProtAcc	P67809

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0017148	Negative regulation of translation
GO:0006417	Regulation of translation
GO:0045727	Positive regulation of translation
GO:0002181	Cytoplasmic translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	YBX1	GO:0006355	regulation of transcription, DNA-templated	18809583
Hgene	YBX1	GO:0045944	positive regulation of transcription by RNA polymerase II	18809583
Hgene	YBX1	GO:0048255	mRNA stabilization	31358969
Hgene	YBX1	GO:1990428	miRNA transport	27559612

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
YBX1	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'YBX1[title] AND translation [title] AND human.'

Gene	Title	PMID
YBX1	YBX1 mediates translation of oncogenic transcripts to control cell competition in AML	34465866

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000321358	43161869	43161959	In-frame
ENST00000321358	43162312	43162615	In-frame

Exon skipping position in the amino acid sequence.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	Len(transcript seq)	Exon skip start (mRNA)	Exon Skip end (mRNA)	Len(amino acid seq)	Exon skip start (AA)	Exon Skip end (AA)
ENST00000321358	43161869	43161959	1531	404	493	324	88	118
ENST00000321358	43162312	43162615	1531	494	796	324	118	219

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc	Exon skip start (AA)	Exon Skip end (AA)	Function feature start (AA)	Function feature end (AA)	Functional feature type	Functional feature desc.
P67809	118	219	2	324	Chain	ID=PRO_0000100219;Note=Nuclease-sensitive element-binding protein 1
P67809	88	118	2	324	Chain	ID=PRO_0000100219;Note=Nuclease-sensitive element-binding protein 1
P67809	118	219	61	125	Domain	Note=CSD
P67809	88	118	61	125	Domain	Note=CSD
P67809	118	219	219	220	Site	Note=Cleavage%3B by 20S proteasomal protease
P67809	88	118	102	102	Modified residue	Note=Phosphoserine%3B by PKB/AKT1;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:19690332,ECO:0000269\|PubMed:15806160;Dbxref=PMID:19690332,PMID:15806160
P67809	118	219	162	162	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:15592455;Dbxref=PMID:15592455
P67809	118	219	165	165	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000269\|Ref.6;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID:23186163
P67809	118	219	167	167	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID:24275569
P67809	118	219	174	174	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:17081983,PMID:18669648,PMID:19690332,PMID:20068231,PMID:21406692,PMID:23186163,PMID:24275569
P67809	118	219	176	176	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:17081983,PMID:18669648,PMID:19690332,PMID:20068231,PMID:21406692,PMID:23186163,PMID:24275569
P67809	118	219	137	137	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18851979;Dbxref=PMID:18851979
P67809	88	118	102	102	Mutagenesis	Note=Loss of phosphorylation by PKB/AKT1. Inhibits translocation to the nucleus and tumor cell growth. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15806160;Dbxref=PMID:15806160
P67809	118	219	120	120	Sequence conflict	Note=A->E;Ontology_term=ECO:0000305;evidence=ECO:0000305
P67809	88	118	88	90	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H95
P67809	88	118	108	115	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H95
P67809	118	219	117	125	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H95
P67809	88	118	117	125	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1H95

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
BRCA	YBX1	1.10467241966451	4.8741280959683e-05
KICH	YBX1	1.86923259160472	8.16583633422851e-06

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type	Gene	miRNA	TargetScan binding score (Context++ score percentile)	Coefficient	Pvalue
CHOL	YBX1	hsa-miR-153-3p	97	-0.302503293807642	0.0438340496370688

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type	Gene	methyl group b	methyl group a	DEG pval	avg methyl in b	avg methyl in a	avg exp in b	avg exp in a
BRCA	YBX1	1	2	0.0129343495102511	0.189539336249035	0.21955741469267	0.100482673654256	0.223648205113886

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
ESCA	YBX1	0.065563761	0.033813372

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with YBX1 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type	Gene group	Translation factor	Correlated gene	Coefficient	Pvalue
KICH	Cell metabolism gene	YBX1	GNB1	0.804597608	7.47E-22
KICH	Cell metabolism gene	YBX1	ALG6	0.806344904	5.22E-22
KICH	Cell metabolism gene	YBX1	PSMB2	0.816988965	5.41E-23
KICH	Cell metabolism gene	YBX1	TXNDC12	0.817926828	4.40E-23
KICH	Cell metabolism gene	YBX1	PSMA5	0.84550435	5.57E-26
KICH	Cell metabolism gene	YBX1	ENO1	0.851296237	1.16E-26
KICH	Epifactor	YBX1	RBBP4	0.807320082	4.26E-22
KICH	Epifactor	YBX1	HDGF	0.811354814	1.83E-22
KICH	Epifactor	YBX1	MEAF6	0.827333829	5.16E-24
KICH	IUPHAR	YBX1	PSMB2	0.816988965	5.41E-23
KICH	TF	YBX1	DZIP1	0.801592161	1.37E-21
PCPG	Cell metabolism gene	YBX1	ELOVL1	0.806157909	5.00E-44
TGCT	Cell metabolism gene	YBX1	AK2	0.807523256	3.90E-37
THYM	Cell metabolism gene	YBX1	MTHFD2L	0.804742961	5.96E-29
THYM	Cell metabolism gene	YBX1	GNG5	0.806986833	3.20E-29
THYM	Cell metabolism gene	YBX1	RRM2	0.807619738	2.68E-29
THYM	Cell metabolism gene	YBX1	POLE2	0.812418685	6.87E-30
THYM	Cell metabolism gene	YBX1	SNRPG	0.823426566	2.59E-31
THYM	Cell metabolism gene	YBX1	ADSL	0.828797266	4.81E-32
THYM	Cell metabolism gene	YBX1	IDH2	0.831468216	2.04E-32
THYM	Cell metabolism gene	YBX1	SEH1L	0.833814809	9.46E-33
THYM	Cell metabolism gene	YBX1	DUT	0.833921925	9.13E-33
THYM	Cell metabolism gene	YBX1	TUBA1B	0.844284767	2.65E-34
THYM	Cell metabolism gene	YBX1	ACAT2	0.850875389	2.43E-35
THYM	CGC	YBX1	FANCG	0.813594555	4.89E-30
THYM	CGC	YBX1	RAP1GDS1	0.814635236	3.61E-30
THYM	CGC	YBX1	EZH2	0.81889015	1.03E-30
THYM	CGC	YBX1	BLM	0.826094781	1.13E-31
THYM	CGC	YBX1	TCF3	0.827670842	6.88E-32
THYM	CGC	YBX1	SET	0.828511358	5.27E-32
THYM	CGC	YBX1	IDH2	0.831468216	2.04E-32
THYM	CGC	YBX1	SFPQ	0.836690157	3.63E-33
THYM	CGC	YBX1	FEN1	0.83837088	2.06E-33
THYM	CGC	YBX1	EWSR1	0.880468458	1.05E-40
THYM	Epifactor	YBX1	CENPA	0.800995667	1.65E-28
THYM	Epifactor	YBX1	HJURP	0.806422318	3.75E-29
THYM	Epifactor	YBX1	AURKB	0.810205728	1.29E-29
THYM	Epifactor	YBX1	AURKA	0.816131155	2.33E-30
THYM	Epifactor	YBX1	RAD54L	0.816987931	1.81E-30
THYM	Epifactor	YBX1	EZH2	0.81889015	1.03E-30
THYM	Epifactor	YBX1	CDK1	0.81894496	1.01E-30
THYM	Epifactor	YBX1	ASF1B	0.8236591	2.41E-31
THYM	Epifactor	YBX1	SET	0.828511358	5.27E-32
THYM	Epifactor	YBX1	RAD51	0.832381327	1.51E-32
THYM	Epifactor	YBX1	CHEK1	0.833063317	1.21E-32
THYM	Epifactor	YBX1	H2AFY	0.834233477	8.24E-33
THYM	Epifactor	YBX1	SFPQ	0.836690157	3.63E-33
THYM	Epifactor	YBX1	UBE2T	0.839242375	1.53E-33
THYM	Epifactor	YBX1	CHAF1A	0.841559272	6.89E-34
THYM	Epifactor	YBX1	CBX3	0.844782601	2.22E-34
THYM	Epifactor	YBX1	VRK1	0.854733527	5.69E-36
THYM	Epifactor	YBX1	PCNA	0.87167886	5.65E-39
THYM	Epifactor	YBX1	H2AFZ	0.893365035	1.65E-43
THYM	IUPHAR	YBX1	MAP2K6	0.801951029	1.28E-28
THYM	IUPHAR	YBX1	RRM2	0.807619738	2.68E-29
THYM	IUPHAR	YBX1	AURKB	0.810205728	1.29E-29
THYM	IUPHAR	YBX1	AURKA	0.816131155	2.33E-30
THYM	IUPHAR	YBX1	EZH2	0.81889015	1.03E-30
THYM	IUPHAR	YBX1	MELK	0.818931315	1.01E-30
THYM	IUPHAR	YBX1	CDK1	0.81894496	1.01E-30
THYM	IUPHAR	YBX1	IDH2	0.831468216	2.04E-32
THYM	IUPHAR	YBX1	CHEK1	0.833063317	1.21E-32
THYM	IUPHAR	YBX1	ACAT2	0.850875389	2.43E-35
THYM	IUPHAR	YBX1	VRK1	0.854733527	5.69E-36
THYM	Kinase	YBX1	MAP2K6	0.801951029	1.28E-28
THYM	Kinase	YBX1	AURKB	0.810205728	1.29E-29
THYM	Kinase	YBX1	AURKA	0.816131155	2.33E-30
THYM	Kinase	YBX1	MELK	0.818931315	1.01E-30
THYM	Kinase	YBX1	CDK1	0.81894496	1.01E-30
THYM	Kinase	YBX1	CHEK1	0.833063317	1.21E-32
THYM	Kinase	YBX1	VRK1	0.854733527	5.69E-36
THYM	TF	YBX1	CENPA	0.800995667	1.65E-28
THYM	TF	YBX1	MYBL2	0.813609989	4.87E-30
THYM	TF	YBX1	TCF3	0.827670842	6.88E-32
THYM	TSG	YBX1	PTPN2	0.803917827	7.47E-29
THYM	TSG	YBX1	FANCG	0.813594555	4.89E-30
THYM	TSG	YBX1	EZH2	0.81889015	1.03E-30
THYM	TSG	YBX1	BLM	0.826094781	1.13E-31
THYM	TSG	YBX1	TCF3	0.827670842	6.88E-32
THYM	TSG	YBX1	CHEK1	0.833063317	1.21E-32
UCS	Cell metabolism gene	YBX1	MTHFD2L	0.804742961	5.96E-29
UCS	Cell metabolism gene	YBX1	GNG5	0.806986833	3.20E-29
UCS	Cell metabolism gene	YBX1	RRM2	0.807619738	2.68E-29
UCS	Cell metabolism gene	YBX1	POLE2	0.812418685	6.87E-30
UCS	Cell metabolism gene	YBX1	SNRPG	0.823426566	2.59E-31
UCS	Cell metabolism gene	YBX1	ADSL	0.828797266	4.81E-32
UCS	Cell metabolism gene	YBX1	IDH2	0.831468216	2.04E-32
UCS	Cell metabolism gene	YBX1	SEH1L	0.833814809	9.46E-33
UCS	Cell metabolism gene	YBX1	DUT	0.833921925	9.13E-33
UCS	Cell metabolism gene	YBX1	TUBA1B	0.844284767	2.65E-34
UCS	Cell metabolism gene	YBX1	ACAT2	0.850875389	2.43E-35
UCS	CGC	YBX1	FANCG	0.813594555	4.89E-30
UCS	CGC	YBX1	RAP1GDS1	0.814635236	3.61E-30
UCS	CGC	YBX1	EZH2	0.81889015	1.03E-30
UCS	CGC	YBX1	BLM	0.826094781	1.13E-31
UCS	CGC	YBX1	TCF3	0.827670842	6.88E-32
UCS	CGC	YBX1	SET	0.828511358	5.27E-32
UCS	CGC	YBX1	IDH2	0.831468216	2.04E-32
UCS	CGC	YBX1	SFPQ	0.836690157	3.63E-33
UCS	CGC	YBX1	FEN1	0.83837088	2.06E-33
UCS	CGC	YBX1	EWSR1	0.880468458	1.05E-40
UCS	Epifactor	YBX1	CENPA	0.800995667	1.65E-28
UCS	Epifactor	YBX1	HJURP	0.806422318	3.75E-29
UCS	Epifactor	YBX1	AURKB	0.810205728	1.29E-29
UCS	Epifactor	YBX1	AURKA	0.816131155	2.33E-30
UCS	Epifactor	YBX1	RAD54L	0.816987931	1.81E-30
UCS	Epifactor	YBX1	EZH2	0.81889015	1.03E-30
UCS	Epifactor	YBX1	CDK1	0.81894496	1.01E-30
UCS	Epifactor	YBX1	ASF1B	0.8236591	2.41E-31
UCS	Epifactor	YBX1	SET	0.828511358	5.27E-32
UCS	Epifactor	YBX1	RAD51	0.832381327	1.51E-32
UCS	Epifactor	YBX1	CHEK1	0.833063317	1.21E-32
UCS	Epifactor	YBX1	H2AFY	0.834233477	8.24E-33
UCS	Epifactor	YBX1	SFPQ	0.836690157	3.63E-33
UCS	Epifactor	YBX1	UBE2T	0.839242375	1.53E-33
UCS	Epifactor	YBX1	CHAF1A	0.841559272	6.89E-34
UCS	Epifactor	YBX1	CBX3	0.844782601	2.22E-34
UCS	Epifactor	YBX1	VRK1	0.854733527	5.69E-36
UCS	Epifactor	YBX1	PCNA	0.87167886	5.65E-39
UCS	Epifactor	YBX1	H2AFZ	0.893365035	1.65E-43
UCS	IUPHAR	YBX1	MAP2K6	0.801951029	1.28E-28
UCS	IUPHAR	YBX1	RRM2	0.807619738	2.68E-29
UCS	IUPHAR	YBX1	AURKB	0.810205728	1.29E-29
UCS	IUPHAR	YBX1	AURKA	0.816131155	2.33E-30
UCS	IUPHAR	YBX1	EZH2	0.81889015	1.03E-30
UCS	IUPHAR	YBX1	MELK	0.818931315	1.01E-30
UCS	IUPHAR	YBX1	CDK1	0.81894496	1.01E-30
UCS	IUPHAR	YBX1	IDH2	0.831468216	2.04E-32
UCS	IUPHAR	YBX1	CHEK1	0.833063317	1.21E-32
UCS	IUPHAR	YBX1	ACAT2	0.850875389	2.43E-35
UCS	IUPHAR	YBX1	VRK1	0.854733527	5.69E-36
UCS	Kinase	YBX1	MAP2K6	0.801951029	1.28E-28
UCS	Kinase	YBX1	AURKB	0.810205728	1.29E-29
UCS	Kinase	YBX1	AURKA	0.816131155	2.33E-30
UCS	Kinase	YBX1	MELK	0.818931315	1.01E-30
UCS	Kinase	YBX1	CDK1	0.81894496	1.01E-30
UCS	Kinase	YBX1	CHEK1	0.833063317	1.21E-32
UCS	Kinase	YBX1	VRK1	0.854733527	5.69E-36
UCS	TF	YBX1	CENPA	0.800995667	1.65E-28
UCS	TF	YBX1	MYBL2	0.813609989	4.87E-30
UCS	TF	YBX1	TCF3	0.827670842	6.88E-32
UCS	TSG	YBX1	PTPN2	0.803917827	7.47E-29
UCS	TSG	YBX1	FANCG	0.813594555	4.89E-30
UCS	TSG	YBX1	EZH2	0.81889015	1.03E-30
UCS	TSG	YBX1	BLM	0.826094781	1.13E-31
UCS	TSG	YBX1	TCF3	0.827670842	6.88E-32
UCS	TSG	YBX1	CHEK1	0.833063317	1.21E-32

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
COAD	YBX1	HNRNPU	-3.25414367586013	0.000109195709228516
LIHC	YBX1	APEX1	-1.68437666096235	0.000122033393260438
STAD	YBX1	DHX9	-1.35515869279777	0.00016188295558095
HNSC	YBX1	TJP1	-1.15535387145194	0.000182808133786239
LIHC	YBX1	EWSR1	-1.00920017153145	0.000263325268073385
BLCA	YBX1	DHX9	2.25372387794619	0.00026702880859375
KICH	YBX1	HNRNPU	1.45270865891102	0.000376403331756592
PRAD	YBX1	HNRNPU	-3.59255010200453	0.00074054058184854
ESCA	YBX1	APEX1	-1.26165583937124	0.0009765625
BRCA	YBX1	APEX1	-1.53190486575975	0.00101019870485577
KICH	YBX1	EWSR1	1.22318794588959	0.00202512741088867
STAD	YBX1	SYNCRIP	-3.24695040489934	0.00222697434946895
KIRP	YBX1	TJP1	-2.27440782036625	0.00337919034063816
CHOL	YBX1	MECP2	-3.96154525072953	0.00390625
UCEC	YBX1	APEX1	3.00090809450605	0.015625
UCEC	YBX1	TP53	2.03295038376694	0.015625
STAD	YBX1	MECP2	-1.59518667419429	0.017460348084569
ESCA	YBX1	EWSR1	-3.15606244879581	0.0185546875
ESCA	YBX1	MECP2	-1.74512825097952	0.0419921875
BLCA	YBX1	EWSR1	1.34714628964121	0.0445594787597656
LUAD	YBX1	APEX1	-4.30098223374594	1.10656371043093e-09
LUSC	YBX1	APEX1	-6.27919186634577	1.23820220972979e-08
KIRC	YBX1	APEX1	-1.11842678842094	1.53660407930827e-06
BRCA	YBX1	TJP1	-4.67254320606445	1.65203581003695e-14
STAD	YBX1	HNRNPU	-1.26566952320815	2.26888805627823e-05
LIHC	YBX1	HNRNPU	-1.06098658215773	2.35319665208461e-06
THCA	YBX1	SYNCRIP	-3.15946429809988	2.46790521879123e-10
LUAD	YBX1	TJP1	-1.96770566983781	2.83612198579349e-08
LIHC	YBX1	NOTCH3	-1.54988089135321	2.90698422155078e-09
THCA	YBX1	NOTCH3	-1.66471565709683	3.03520282946109e-06
LUSC	YBX1	TJP1	-3.26126941857339	3.6218774072117e-09
KIRC	YBX1	TJP1	-2.01258303787563	4.47117775598177e-07
KIRC	YBX1	TP53	-1.43050981150632	4.58942580328929e-09
KIRP	YBX1	MECP2	-3.19416092672143	4.5965425670147e-06
PRAD	YBX1	TJP1	1.07626720993625	6.13785511132143e-06
THCA	YBX1	TP53	-1.81960143635647	6.18215597921662e-07
COAD	YBX1	NOTCH3	-1.49847220042772	7.02440738677979e-05
KIRC	YBX1	MECP2	-1.34839281488966	8.04051937698217e-06
KICH	YBX1	MECP2	2.04803292047028	8.34465026855468e-07
STAD	YBX1	EWSR1	-1.73111038863938	9.0546440333128e-05

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with YBX1

SRSF9, RNU11, ANKRD2, TP53, CTCF, FUS, IREB2, PCNA, TFAP2A, RBBP6, MEPCE, RPAP2, CDK9, KHDRBS2, MECP2, GIGYF2, HABP4, SRRM2, tat, HIST1H1C, NPM1, POU5F1, AGO4, Mapk13, NOP56, SIRT1, CALM1, MAPK1, GSK3B, SREK1, RAD21, RPS6KA1, RPS6KA3, SF3A2, ARRB1, ARRB2, EWSR1, IRF1, FBXO33, CUL1, NFX1, CUL3, CUL4B, CUL2, COPS5, CAND1, NEDD8, HNRNPD, GZF1, HNRNPK, HNRNPU, SNRPD1, SNRPD2, SF3B3, SF3B2, HNRNPA2B1, SNRPA1, PHF5A, ALYREF, SNRNP200, EEF1A1, SYNCRIP, PRKDC, UBAP2L, HSPA5, SSBP1, LMAN1, ATP6V1E1, PSMC2, PSMB2, PSMA2, PSMB5, PSMA4, FLOT1, EIF2S1, PSMC4, PSMB4, HSPA1A, ESR1, BARD1, BRCA1, PAXIP1, MAGOH, EIF4A3, SMURF1, EP300, APEX1, MYC, FN1, LSM3, SMU1, CSNK2A1, IFIT1, IFIT2, IFIT3, IQCB1, NOS2, IL7R, ITGA4, CBX6, CBX8, PAN2, IGSF8, ICAM1, ACTA2, HLA-C, JAM2, LCP2, TRAF6, FBXO6, PRPF40A, APBB1, HNRNPAB, ILF2, MAP2, NMT1, PTBP1, RPL23A, TUBA4A, TUBB, NELFB, DDX1, DIMT1, DYNC1H1, DYNC1I2, DYNC1LI2, EIF2B2, EIF3K, FKBP3, G3BP1, PA2G4, SMURF2, IVNS1ABP, STAU1, SPRTN, AURKA, AKT1, CUL7, OBSL1, CCDC8, EZH2, SUZ12, RNF2, BMI1, RPL6, RPS2, RPS6KB2, FBXW11, UNK, MAEL, NTRK1, C1QBP, COX5A, EIF3I, NDUFA9, SKIV2L2, MATR3, RNU12, CASP8, XPO1, SORT1, BAG6, C1qbp, Cbx1, FBXW7, MACROD1, HACE1, VPS37B, VAPB, EXOSC9, AP2A2, CAPRIN1, MCM5, CDC20, SRP72, SMC2, HDLBP, USP10, SRPK2, BUB3, TSG101, Ksr1, U2AF2, C3orf17, EGFR, RRS1, ZC3HAV1, H2AFX, BHLHA15, E4F1, ZCRB1, SART3, ZNF324B, GLTSCR2, RPSA, THUMPD1, SURF2, NCL, CYLD, TRIM25, UBE2A, HEY1, LMNA, YAP1, DCAF4L2, MYCN, PCBP1, TMPO, CTNNB1, GSK3A, IQGAP1, API5, BMP4, KRAS, TRIP4, YAF2, HIF1A, PRPF8, EFTUD2, AAR2, PIH1D1, TNIP2, RNF4, CHD3, LARP7, RNF31, SPDL1, RIOK1, HEXIM1, FERMT2, AGO2, SNAI1, AGR2, RECQL4, PIK3R1, GPC1, REST, ZFP36L2, WDR76, HIST1H4A, HIST1H2AB, VCP, METTL14, KIAA1429, RC3H1, RC3H2, ATG16L1, ACTC1, PHB, FAF1, RBX1, MAPT, NR2C2, PPP1CC, MTDH, OASL, SNRNP70, Dppa3, ITFG1, ARAF, PPP1CA, BIRC3, BRD7, SOX2, LRRK2, CMTR1, OTUD3, ARIH2, PLEKHA4, PINK1, TFCP2, FANCD2, NGB, HCVgp1, MIRLET7A1, MIRLET7A2, MIRLET7A3, MIRLET7B, MIRLET7C, MIRLET7D, MIRLET7E, MIRLET7F1, MIRLET7F2, MIRLET7G, MIRLET7I, MIR98, MIR1-1, MIR1-2, MIR7-1, MIR7-2, MIR7-3, MIR9-1, MIR9-2, MIR9-3, MIR10B, MIR15A, MIR15B, MIR16-1, MIR16-2, MIR17, MIR18A, MIR18B, MIR19A, MIR19B1, MIR19B2, MIR20A, MIR20B, MIR21, MIR25, MIR29A, MIR29B1, MIR29B2, MIR29C, MIR31, MIR34A, MIR34B, MIR34C, MIR92A1, MIR92A2, MIR93, MIR106A, MIR106B, MIR107, MIR122, MIR128-1, MIR128-2, MIR138-1, MIR138-2, MIR140, MIR141, MIR143, MIR145, MIR155, MIR199A1, MIR199A2, MIR200A, MIR200B, MIR200C, MIR205, MIR206, MIR214, MIR221, MIR222, MIR363, MIR429, MIR451A, ZC3H18, DUSP1, NEK1, DUX4, CIT, ANLN, AURKB, CHMP4C, ECT2, KIF14, KIF20A, KIF23, PRC1, GRSF1, LRRC59, INS, NDN, RBM45, N, Apc2, DANCR, RBM39, FBP1, MKRN1, LGALS9, IFI16, INSIG1, INSIG2, RIN3, EIF3H, ZNF514, MRPL21, TRA2B, NHP2, MRPL17, PABPC4, LIN28A, MRPL18, SSB, MRPL19, PRDM9, UBE2V2, PABPC1, MRPL30, SPICE1, DDX58, OGT, BAG5, SPOP, ISG15, PARK2, UFL1, DDRGK1, NR4A1, AP2B1, RPS20, SERBP1, TRIM37, TLE4, CDC5L, PLRG1, BCAS2, PRPF19, VPS35, UBQLN1, FZR1, WDR5, PAGE4, NUDCD2, TRIM28, THAP3, TRUB2, SRSF6, MRPS25, MTERF3, MRPS18A, MRPS18C, RPL13A, APOBEC3F, HIST1H1A, BRIX1, MRPS5, MRPS33, RPS3A, MRPL16, RSL1D1, CHCHD2, RPS19, ICT1, NSA2, MRPL3, MAGEB2, UTP23, RPS10, RPS9, MRPL22, LARP4B, MRPL32, MRPL52, MRPL37, HIST2H2AC, RPL3, MRPL11, MRPL1, MRPL40, RPS16, DDX21, GADD45GIP1, RBMS2, MRPL27, SURF6, RPS6, PPIG, LARP1, MRPL42, MRPS18B, AGO1, MRPS11, HNRNPCL1, ZC3H11A, MRPS30, MRPL51, MRPL24, PURG, MRPS2, SRSF1, RPL31, HNRNPC, H1FNT, RBM19, GLI4, PTBP3, PTCD1, MRPS7, UPF1, RPL7A, PABPC4L, LIN28B, RPL7, RBM23, ABT1, MRPS31, RPF1, PURB, MRPL41, YBX3, MRPL45, CHCHD10, MRPL33, MRPS10, HIST1H2AM, ZC3H8, DKC1, CMSS1, HNRNPUL2, ZFR, KRR1, DAP3, RPL36AL, YBX2, GNL2, TRIM71, MRPS24, RPS3, NIFK, MRPL50, HIST1H2AG, HIST1H1E, NEIL1, ZCCHC9, NOP10, RPL4, ZNF777, MRPL20, DDX54, RPS8, MRPL28, MRPL2, HIST1H1D, FGF13, MRPL44, WHSC1, MRPL10, PTCD3, LARP1B, REXO4, RPL19, MRPL47, SRSF5, MRPS34, MRPL13, PABPC5, RPL13, HIST1H1T, HIST1H1B, RPL22, MRPS22, ZBTB48, PAIP2B, FTSJ3, KRI1, RPSAP58, FASTKD2, ZNF668, ELAVL2, RPL23AP32, RPL7L1, HIST1H2AE, H2AFB3, ZNF184, LLPH, RBMXL1, RPL26, RPS24, NUPL2, MRPL39, MRPS28, SRSF3, MRPL4, MRPL49, MRPL38, MRPL9, NGRN, PRR3, RPL26L1, MRPL23, RPL17, MRPS21, MRPL57, H2AFB2, RNF151, MRPL15, MYBBP1A, MRPS9, FARS2, MRPS27, RPL35, ZNF574, APOBEC3D, ZNF346, PAIP1, MRPL12, SRSF7, GSPT2, RPLP0, ZC3H3, FGFBP1, MRPS17, RPL10, USP47, BTF3, NLRP7, FGD5, APOBEC3B, CCNF, NBR1, CALCOCO2, SQSTM1, CPEB1, MAGEL2, ZEB1,

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Mutations

Clinically associated variants from ClinVar.

Gene

Chr

Position

RefSeq

VarSeq

RefSeeq

VarType

Pathogenic

Disease

VarInfo

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
YBX1	PCPG	chr1	43166630	43166630	G	A	Missense_Mutation	p.D307N	3
YBX1	ESCA	chr1	43162401	43162401	A	G	Missense_Mutation	p.Y148C	3
YBX1	ESCA	chr1	43166567	43166567	A	G	Missense_Mutation	p.N286D	3
YBX1	ESCA	chr1	43162401	43162401	A	G	Missense_Mutation		2
YBX1	BRCA	chr1	43166508	43166508	A	G	Missense_Mutation	p.N266S	2
YBX1	PCPG	chr1	43162410	43162410	G	C	Missense_Mutation	p.R151P	2
YBX1	ESCA	chr1	43166604	43166604	A	T	Missense_Mutation		2
YBX1	UCEC	chr1	43162425	43162425	G	A	Missense_Mutation	p.R156H	2
YBX1	ESCA	chr1	43166604	43166604	A	T	Missense_Mutation	p.Q298L	2
YBX1	UCEC	chr1	43162438	43162438	A	G	Silent	p.K210R	2
YBX1	LUAD	chr1	43166670	43166670	A	T	Missense_Mutation	p.Q320L	2
YBX1	CESC	chr1	43162569	43162569	G	A	Missense_Mutation		2
YBX1	UCEC	chr1	43166469	43166469	G	C	Missense_Mutation	p.R253T	2
YBX1	LUAD	chr1	43162350	43162350	T	C	Missense_Mutation	p.V131A	2
YBX1	COAD	chr1	43162382	43162382	C	T	Missense_Mutation	p.R142C	2
YBX1	SARC	chr1	43166655	43166655	C	A	Missense_Mutation		2
YBX1	UCEC	chr1	43166546	43166546	C	T	Missense_Mutation	p.R279C	2
YBX1	HNSC	chr1	43166568	43166568	A	G	Missense_Mutation	p.N286S	2
YBX1	UCEC	chr1	43166559	43166559	G	A	Missense_Mutation	p.R283H	2
YBX1	SKCM	chr1	43166649	43166649	C	T	Missense_Mutation	p.S313L	2
YBX1	KIRP	chr1	43166452	43166452	G	A	Silent	p.R247R	2
YBX1	KIRP	chr1	43166460	43166460	C	T	Missense_Mutation	p.P250L	2
YBX1	LIHC	chr1	43162928	43162928	C	T	Silent		2
YBX1	LIHC	chr1	43162928	43162928	C	T	Silent	p.F245F	2
YBX1	ESCA	chr1	43166567	43166567	A	G	Missense_Mutation		2
YBX1	STAD	chr1	43162317	43162317	C	T	Missense_Mutation	p.A120V	2
YBX1	LIHC	chr1	43166611	43166612	-	A	Frame_Shift_Ins	p.R301fs	1
YBX1	BLCA	chr1	43162472	43162472	G	A	Missense_Mutation	p.E172K	1
YBX1	STAD	chr1	43166532	43166532	A	C	Missense_Mutation	p.Q274P	1
YBX1	LIHC	chr1	43149096	43149096	A	-	Frame_Shift_Del	p.V63fs	1
YBX1	LUAD	chr1	43166675	43166675	G	A	Missense_Mutation	p.G322R	1
YBX1	CESC	chr1	43162918	43162918	G	C	Missense_Mutation		1
YBX1	PRAD	chr1	43162925	43162925	A	C	Silent	p.R244R	1
YBX1	PRAD	chr1	43162406	43162406	C	T	Missense_Mutation	p.R150C	1
YBX1	HNSC	chr1	43166624	43166624	G	C	Missense_Mutation		1
YBX1	HNSC	chr1	43166568	43166568	A	G	Missense_Mutation		1
YBX1	LUAD	chr1	43166554	43166555	CC	AA	Nonsense_Mutation	p.281_282YR>*S	1
YBX1	COAD	chr1	43162398	43162398	G	A	Missense_Mutation	p.R147H	1
YBX1	SARC	chr1	43166655	43166655	C	A	Missense_Mutation	p.A315D	1
YBX1	LUSC	chr1	43161906	43161906	C	T	Missense_Mutation	p.R101C	1
YBX1	COAD	chr1	43162856	43162856	T	C	Silent	p.A221A	1
YBX1	UVM	chr1	43166559	43166559	G	T	Missense_Mutation	p.R283L	1
YBX1	OV	chr1	43149119	43149119	G	T	Missense_Mutation	p.G71V	1
YBX1	DLBC	chr1	43149084	43149084	T	C	Silent	p.V59V	1
YBX1	SKCM	chr1	43166637	43166637	C	T	Missense_Mutation	p.P309L	1
YBX1	ACC	chr1	43166582	43166582	C	T	Missense_Mutation	p.R291C	1
YBX1	OV	chr1	43162404	43162404	C	G	Missense_Mutation	p.P149R	1
YBX1	SKCM	chr1	43166585	43166585	C	T	Missense_Mutation	p.P292S	1
YBX1	BLCA	chr1	43166588	43166588	G	A	Missense_Mutation		1
YBX1	OV	chr1	43162857	43162857	G	C	Missense_Mutation	p.D222H	1
YBX1	SKCM	chr1	43162381	43162381	C	T	Silent	p.D141D	1
YBX1	BLCA	chr1	43166588	43166588	G	A	Missense_Mutation	p.E293K	1
YBX1	OV	chr1	43166659	43166659	C	T	Silent	p.P316	1

Copy number variation (CNV) of YBX1
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across YBX1
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
99928	OV	TCGA-24-1847	ACYP2	chr2	54365885	+	YBX1	chr1	43166451	+
99928	COAD	TCGA-AA-A03F-01A	ATP5D	chr19	1241982	+	YBX1	chr1	43159171	+
99928	OV	TCGA-24-2020-01A	CCDC30	chr1	42929569	+	YBX1	chr1	43159161	+
99928	Non-Cancer	ERR188417	FOXJ3	chr1	42776721	-	YBX1	chr1	43159161	+
99928	STAD	TCGA-BR-8366-01A	HCP5	chr6	31368540	+	YBX1	chr1	43166452	+
99928	READ	TCGA-DC-6157	NUPL2	chr7	23226765	+	YBX1	chr1	43149073	+
99928	N/A	BI491156	PTPRT	chr20	41033858	+	YBX1	chr1	43168020	-
99928	PRAD	TCGA-M7-A71Z	YBX1	chr1	43149137	+	AXDND1	chr1	179437577	+
99928	PRAD	TCGA-M7-A71Z	YBX1	chr1	43149137	+	AXDND1	chr1	179437578	+
99928	N/A	CD580594	YBX1	chr1	43162433	+	CALN1	chr7	71486081	+
99928	BRCA	TCGA-D8-A13Y-01A	YBX1	chr1	43166717	+	MED8	chr1	43851897	-
99928	N/A	BU536214	YBX1	chr1	43148360	+	NCBP2	chr3	196663955	-
99928	N/A	BF331397	YBX1	chr1	43162615	+	YBX1	chr1	43161918	+

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
KIRC	YBX1	2.64967984821531e-05	0.00074
LIHC	YBX1	4.32583478329692e-05	0.0012

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LGG	YBX1	0.000927023079444873	0.028
BRCA	YBX1	1.04239536241671e-08	3.4e-07
SKCM	YBX1	0.0487156485942801	1
ESCA	YBX1	0.013048653995141	0.38
THYM	YBX1	0.000155715303627923	0.005
SARC	YBX1	0.000306624874304338	0.0095

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID	Disease Name	# PubMeds	Disease source
C0006142	Malignant neoplasm of breast	1	CTD_human
C0007102	Malignant tumor of colon	1	CTD_human
C0023893	Liver Cirrhosis, Experimental	1	CTD_human
C0678222	Breast Carcinoma	1	CTD_human
C1257931	Mammary Neoplasms, Human	1	CTD_human
C4704874	Mammary Carcinoma, Human	1	CTD_human