EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000159352 (Gene tree)
Gene ID: 5710
Gene Symbol: PSMD4
Alias: S5A|AF-1|AF|Rpn10
Full Name: proteasome 26S subunit, non-ATPase 4
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 12,780 bases
Position: chr1:151,254,700-151,267,479
Accession: 9561
RBP type: non-canonical RBP
Summary: The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes one of the non-ATPase subunits of the 19S regulator lid. Pseudogenes have been identified on chromosomes 10 and 21. [provided by RefSeq, Jul 2008]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
29431736	Capturing the interactome of newly transcribed RNA	RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
22658674	Insights into RNA biology from an atlas of mammalian mRNA-binding proteins	RIC & Hela	2012 May 31	Castello A	DOI: 10.1016/j.cell.2012.04.031
27453046	Comprehensive Identification of RNA-Binding Domains in Human Cells	RIC & Hela	2016 Aug 18	Castello A	DOI: 10.1016/j.molcel.2016.06.029

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000445776	PSMD4-205	703	-	ENSP00000388089	193 (aa)	-	H0Y3Y9
ENST00000461434	PSMD4-207	801	-	-	- (aa)	-	-
ENST00000469786	PSMD4-209	408	-	-	- (aa)	-	-
ENST00000470396	PSMD4-210	338	-	-	- (aa)	-	-
ENST00000453615	PSMD4-206	371	-	ENSP00000396633	84 (aa)	-	H0Y561
ENST00000368884	PSMD4-202	1350	XM_017001856	ENSP00000357879	377 (aa)	XP_016857345	P55036
ENST00000437736	PSMD4-204	787	-	ENSP00000414499	203 (aa)	-	A6PVX3
ENST00000427779	PSMD4-203	649	-	ENSP00000406408	39 (aa)	-	H7C2J9
ENST00000476855	PSMD4-211	1232	-	-	- (aa)	-	-
ENST00000462970	PSMD4-208	900	-	-	- (aa)	-	-
ENST00000491857	PSMD4-212	461	-	-	- (aa)	-	-
ENST00000368881	PSMD4-201	1333	XM_006711464	ENSP00000357876	380 (aa)	XP_006711527	Q5VWC4

Gene Model

Click here to download ENSG00000159352's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa03050	Proteasome	KEGG
hsa05169	Epstein-Barr virus infection	KEGG

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000159352's network

* RBP PPI network refers to all genes directly bind to RBP

Orthologs identified by RBPome

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000159352	PSMD4	100	100.000	ENSMUSG00000005625	Psmd4	97	96.458	Mus_musculus
ENSG00000159352	PSMD4	99	48.131	YHR200W	RPN10	88	50.424	Saccharomyces_cerevisiae

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000165	MAPK cascade	-	TAS	Process
GO:0000209	protein polyubiquitination	-	TAS	Process
GO:0000502	proteasome complex	17323924.	IDA	Component
GO:0002223	stimulatory C-type lectin receptor signaling pathway	-	TAS	Process
GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	-	TAS	Process
GO:0003723	RNA binding	22658674.	HDA	Function
GO:0005515	protein binding	10488153.11146632.15147878.16990800.17082820.17139257.17662948.18922472.19490896.19615732.19796170.19798103.20059542.20195357.24811749.25036637.26496610.29290612.29426014.29997244.	IPI	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005654	nucleoplasm	-	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005829	cytosol	21873635.	IBA	Component
GO:0005829	cytosol	-	IDA	Component
GO:0005829	cytosol	-	TAS	Component
GO:0006521	regulation of cellular amino acid metabolic process	-	TAS	Process
GO:0008540	proteasome regulatory particle, base subcomplex	21873635.	IBA	Component
GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	-	TAS	Process
GO:0016579	protein deubiquitination	-	TAS	Process
GO:0022624	proteasome accessory complex	-	ISS	Component
GO:0031145	anaphase-promoting complex-dependent catabolic process	-	TAS	Process
GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	-	TAS	Process
GO:0031593	polyubiquitin modification-dependent protein binding	21873635.	IBA	Function
GO:0033209	tumor necrosis factor-mediated signaling pathway	-	TAS	Process
GO:0038061	NIK/NF-kappaB signaling	-	TAS	Process
GO:0038095	Fc-epsilon receptor signaling pathway	-	TAS	Process
GO:0042802	identical protein binding	16990800.19931242.	IPI	Function
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	21873635.	IBA	Process
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	-	TAS	Process
GO:0043248	proteasome assembly	21873635.	IBA	Process
GO:0043488	regulation of mRNA stability	-	TAS	Process
GO:0043687	post-translational protein modification	-	TAS	Process
GO:0050852	T cell receptor signaling pathway	-	TAS	Process
GO:0055085	transmembrane transport	-	TAS	Process
GO:0060071	Wnt signaling pathway, planar cell polarity pathway	-	TAS	Process
GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	-	TAS	Process
GO:0070498	interleukin-1-mediated signaling pathway	-	TAS	Process
GO:0090090	negative regulation of canonical Wnt signaling pathway	-	TAS	Process
GO:0090263	positive regulation of canonical Wnt signaling pathway	-	TAS	Process
GO:1901990	regulation of mitotic cell cycle phase transition	-	TAS	Process
GO:1902036	regulation of hematopoietic stem cell differentiation	-	TAS	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
24250289	Reduction of angiocidin contributes to decreased HepG2 cell proliferation.	Afr Health Sci	2013 Sep	Guan XG	doi: 10.4314/ahs.v13i3.5.
19519434	The immunomodulatory role of angiocidin, a novel angiogenesis inhibitor.	Curr Pharm Des	2009	Gaurnier-Hausser A	-
16762342	Integrin alpha2beta1 mediates the anti-angiogenic and anti-tumor activities of angiocidin, a novel tumor-associated protein.	Exp Cell Res	2006 Aug 1	Sabherwal Y	-
27033953	Cytoplasmic localization of Nrf2 promotes colorectal cancer with more aggressive tumors via upregulation of PSMD4.	Free Radic Biol Med	2016 Jun	Lin PL	doi: 10.1016/j.freeradbiomed.2016.03.014

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
ACC	chr1	151264005	Missense_Mutation	novel	C87R	0.26
BLCA	chr1	151266391	Missense_Mutation	NA	E283Q	0.12
BLCA	chr1	151265515	Missense_Mutation	NA	P187L	0.46
BLCA	chr1	151267193	Silent	novel	V328V	0.1
BLCA	chr1	151266058	Missense_Mutation	NA	R237W	0.38
BLCA	chr1	151267342	Nonstop_Mutation	novel	378Lext11	0.41
BRCA	chr1	151263929	Silent	rs151089424	L61L	0.21
BRCA	chr1	151266518	Splice_Site	novel	X299_splice	0.35
BRCA	chr1	151266559	Nonsense_Mutation	NA	S312*	0.19
BRCA	chr1	151254764	5'UTR	novel		0.26
BRCA	chr1	151254792	Missense_Mutation	NA	E4Q	0.61
BRCA	chr1	151265522	Silent	rs768195322	L189L	0.06
BRCA	chr1	151267308	Missense_Mutation	rs770584632	G367S	0.53
BRCA	chr1	151254781	5'UTR	novel		0.14
CESC	chr1	151262246	Missense_Mutation	NA	H38Y	0.26
COAD	chr1	151265414	Silent	novel	L153L	0.31
COAD	chr1	151267347	3'UTR	novel		0.32
COAD	chr1	151262184	Missense_Mutation	NA	R17Q	0.26
COAD	chr1	151267466	3'UTR	novel		0.36
COAD	chr1	151267207	Missense_Mutation	novel	E333G	0.15
COAD	chr1	151264019	Silent	rs781264881	R91R	0.4
COAD	chr1	151265475	Missense_Mutation	NA	P174S	0.41
COAD	chr1	151262235	Missense_Mutation	rs768592153	N34S	0.35
ESCA	chr1	151262201	Frame_Shift_Del	novel	*T24Sfs7**	0.05
GBM	chr1	151262259	Missense_Mutation	novel	R42H	0.33
HNSC	chr1	151267173	Missense_Mutation	rs769270518	E322K	0.23
HNSC	chr1	151264855	Silent	novel	G102G	0.18
HNSC	chr1	151262185	Silent	novel	R17R	0.1
KIRC	chr1	151264009	Missense_Mutation	rs761401984	T88M	0.21
KIRP	chr1	151265587	Missense_Mutation	novel	S211I	0.28
LAML	chr1	151265525	Silent	novel	A190A	0.05
LGG	chr1	151265184	Missense_Mutation	rs749225884	R130C	0.14
LIHC	chr1	151265468	Silent	NA	V171V	0.34
LIHC	chr1	151267261	Missense_Mutation	novel	A351G	0.09
LUAD	chr1	151262185	Silent	NA	R17R	0.45
LUAD	chr1	151266549	Missense_Mutation	novel	D309Y	0.52
LUAD	chr1	151265420	Silent	rs769012730	A155A	0.48
LUAD	chr1	151267401	3'UTR	novel		0.37
LUAD	chr1	151265218	Missense_Mutation	novel	I141S	0.11
LUSC	chr1	151254779	5'UTR	novel		0.44
LUSC	chr1	151265442	Missense_Mutation	NA	K163E	0.23
OV	chr1	151266391	Missense_Mutation	novel	E283K	0.07
OV	chr1	151267200	Missense_Mutation	novel	D331Y	0.06
PRAD	chr1	151262184	Missense_Mutation	NA	R17Q	0.15
SARC	chr1	151265181	Frame_Shift_Del	novel	*K129Nfs8**	0.06
SKCM	chr1	151266005	Missense_Mutation	novel	A219V	0.43
SKCM	chr1	151266006	Splice_Region	novel	A219A	0.43
SKCM	chr1	151266074	Missense_Mutation	novel	S242F	0.36
SKCM	chr1	151267283	Silent	novel	S358S	0.26
SKCM	chr1	151267248	Missense_Mutation	NA	P347S	0.97
SKCM	chr1	151265460	Missense_Mutation	NA	H169Y	0.35
STAD	chr1	151267457	3'UTR	novel		0.31
STAD	chr1	151267273	Missense_Mutation	NA	A355D	0.36
UCEC	chr1	151263933	Missense_Mutation	novel	T63P	0.11
UCEC	chr1	151267200	Missense_Mutation	novel	D331N	0.08
UCEC	chr1	151264017	Missense_Mutation	novel	R91C	0.3
UCEC	chr1	151267268	Silent	novel	R353R	0.05
UCEC	chr1	151267284	Missense_Mutation	novel	L359M	0.34
UCEC	chr1	151267456	3'UTR	novel		0.46
UCEC	chr1	151262183	Missense_Mutation	rs755580240	R17W	0.52
UCEC	chr1	151262183	Missense_Mutation	rs755580240	R17W	0.18
UCEC	chr1	151265544	Missense_Mutation	NA	L197M	0.26
UCEC	chr1	151267203	Missense_Mutation	novel	P332S	0.05
UCEC	chr1	151267267	Missense_Mutation	novel	R353Q	0.42
UCEC	chr1	151266533	Silent	rs750811233	A303A	0.4
UCEC	chr1	151264867	Missense_Mutation	novel	K106N	0.55
UCEC	chr1	151267344	3'UTR	novel		0.46
UCEC	chr1	151265454	Missense_Mutation	rs751785323	G167S	0.36
UCEC	chr1	151267395	3'UTR	rs754794543		0.41
UCEC	chr1	151267267	Missense_Mutation	novel	R353Q	0.34
UCEC	chr1	151262182	Missense_Mutation	NA	M16I	0.29
UCEC	chr1	151265501	Silent	novel	A182A	0.14
UCEC	chr1	151265505	Missense_Mutation	novel	I184V	0.22
UCEC	chr1	151262266	Missense_Mutation	novel	N44K	0.25
UCEC	chr1	151266358	Missense_Mutation	rs181572831	R272C	0.24
UCEC	chr1	151264871	Missense_Mutation	rs756640390	R108C	0.1
UCEC	chr1	151264871	Missense_Mutation	rs756640390	R108C	0.39

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
ACC	AMP	0.1333	0.11282
CESC	AMP	0.4814	3.2002e-05
DLBC	DEL	0.0208	0.0017831
ESCA	AMP	0.4022	0.0022446
KIRC	AMP	0.0928	0.059566
LUSC	AMP	0.4291	1.6618e-06
PAAD	AMP	0.2174	0.085665
PCPG	AMP	0.1481	0.00029562
READ	AMP	0.2667	0.025154
SARC	AMP	0.3424	4.3422e-08
SKCM	AMP	0.485	9.6912e-06
TGCT	AMP	0.34	0.088103

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.0001	Kaplan-Meier Survival Analysis
MESO	0.00026	Kaplan-Meier Survival Analysis
ACC	0.00018	Kaplan-Meier Survival Analysis
KIRP	0.0043	Kaplan-Meier Survival Analysis
COAD	0.025	Kaplan-Meier Survival Analysis
LAML	0.00012	Kaplan-Meier Survival Analysis
GBM	0.038	Kaplan-Meier Survival Analysis
LIHC	0.0042	Kaplan-Meier Survival Analysis
LGG	0.011	Kaplan-Meier Survival Analysis
UVM	0.0051	Kaplan-Meier Survival Analysis
OV	0.047	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

PPI

Orthologs

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742