EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000131435 (Gene tree)
Gene ID: 8572
Gene Symbol: PDLIM4
Alias: RIL
Full Name: PDZ and LIM domain 4
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 15,797 bases
Position: chr5:132,257,658-132,273,454
Accession: 16501
RBP type: non-canonical RBP
Summary: This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000463615	PDLIM4-205	582	-	-	- (aa)	-	-
ENST00000484620	PDLIM4-207	456	-	-	- (aa)	-	-
ENST00000474421	PDLIM4-206	1084	-	-	- (aa)	-	-
ENST00000379018	PDLIM4-202	1006	-	ENSP00000368303	246 (aa)	-	P50479
ENST00000253754	PDLIM4-201	2282	XM_017010002	ENSP00000253754	330 (aa)	XP_016865491	P50479
ENST00000462597	PDLIM4-204	767	-	-	- (aa)	-	-
ENST00000418373	PDLIM4-203	538	-	ENSP00000411753	121 (aa)	-	C9J542

Gene Model

Click here to download ENSG00000131435's gene model file

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000131435	rs55722650	5	132271607	T	Mosquito bite size	28199695	[0.039-0.06] unit decrease	0.0490999	EFO_0008378
ENSG00000131435	rs10479001	5	132272028	T	Red cell distribution width	28957414	[0.037-0.076] unit increase	0.0564112	EFO_0005192

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000131435's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0001725	stress fiber	21636573.	IDA	Component
GO:0005515	protein binding	10826496.19307596.21636573.	IPI	Function
GO:0005634	nucleus	10826496.21636573.	IDA	Component
GO:0005737	cytoplasm	21636573.	IDA	Component
GO:0005856	cytoskeleton	21636573.	IDA	Component
GO:0019903	protein phosphatase binding	19307596.	IPI	Function
GO:0030027	lamellipodium	10826496.	IDA	Component
GO:0030054	cell junction	-	IEA	Component
GO:0031532	actin cytoskeleton reorganization	21636573.	IDA	Process
GO:0031901	early endosome membrane	-	IEA	Component
GO:0031905	early endosome lumen	-	ISS	Component
GO:0031941	filamentous actin	10826496.	IDA	Component
GO:0034777	recycling endosome lumen	-	ISS	Component
GO:0042803	protein homodimerization activity	25158098.	IDA	Function
GO:0043197	dendritic spine	-	ISS	Component
GO:0045211	postsynaptic membrane	-	ISS	Component
GO:0046872	metal ion binding	-	IEA	Function
GO:0048471	perinuclear region of cytoplasm	19307596.	IDA	Component
GO:0051393	alpha-actinin binding	20120020.	IPI	Function
GO:0055038	recycling endosome membrane	-	IEA	Component
GO:0098976	excitatory chemical synaptic transmission	-	ISS	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
19212833	PDLIM4, an actin binding protein, suppresses prostate cancer cell growth.	Cancer Invest	2009 Mar	Vanaja DK	doi: 10.1080/07357900802406319.

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
ACC	chr5	132272160	Silent	rs1140552	A308A	0.25
BLCA	chr5	132271855	Silent	rs750840954	P245P	0.13
BLCA	chr5	132271361	Missense_Mutation	novel	E189Q	0.18
BLCA	chr5	132271790	Splice_Site	novel	X224_splice	0.13
BRCA	chr5	132272168	Missense_Mutation	NA	K311M	0.74
BRCA	chr5	132271419	Nonsense_Mutation	novel	S208*	0.4
COAD	chr5	132271661	Intron	novel		0.21
COAD	chr5	132271085	Frame_Shift_Ins	novel	*S169Qfs3**	0.33
COAD	chr5	132272065	Missense_Mutation	NA	E277K	0.38
COAD	chr5	132271034	Silent	novel	G149G	0.17
COAD	chr5	132271526	Intron	novel		0.33
COAD	chr5	132271086	Frame_Shift_Del	NA	*S169Afs50**	0.33
COAD	chr5	132262734	Silent	rs777277749	H73H	0.39
COAD	chr5	132266530	Silent	rs145529462	I104I	0.18
COAD	chr5	132272160	Silent	rs1140552	A308A	0.38
COAD	chr5	132271855	Silent	rs750840954	P245P	0.15
DLBC	chr5	132272218	Missense_Mutation	novel	E328K	0.13
ESCA	chr5	132271708	Intron	novel		0.56
ESCA	chr5	132272089	Missense_Mutation	rs202040278	G285S	0.48
GBM	chr5	132271708	Intron	novel		0.39
KIRC	chr5	132270999	Missense_Mutation	NA	G138R	0.23
KIRC	chr5	132262735	Missense_Mutation	novel	D74Y	0.08
KIRC	chr5	132271879	Silent	rs752956503	P253P	0.6
KIRP	chr5	132271701	Intron	NA		0.21
KIRP	chr5	132266518	Silent	rs774647839	H100H	0.31
KIRP	chr5	132270929	Frame_Shift_Del	novel	*T115Pfs45**	0.47
KIRP	chr5	132271576	Intron	novel		0.42
LIHC	chr5	132271705	Intron	novel		0.07
LIHC	chr5	132271705	Intron	novel		0.27
LIHC	chr5	132271366	Silent	novel	V190V	0.3
LIHC	chr5	132271824	Missense_Mutation	rs557597794	L235H	0.31
LIHC	chr5	132271862	Missense_Mutation	rs766802234	G248S	0.51
LUAD	chr5	132271396	Silent	novel	P200P	0.13
LUAD	chr5	132270933	Missense_Mutation	novel	S116C	0.19
LUAD	chr5	132270959	Silent	novel	T124T	0.18
LUSC	chr5	132271825	Silent	novel	L235L	0.27
LUSC	chr5	132271465	Splice_Region	NA	G223G	0.53
OV	chr5	132272133	Silent	NA	R299R	0.56
OV	chr5	132270928	Missense_Mutation	NA	T114K	0.29
OV	chr5	132270993	Frame_Shift_Del	NA	*P136Hfs24**	0.26
PAAD	chr5	132271516	Intron	novel		0.2
READ	chr5	132271571	Intron	novel		0.3
SKCM	chr5	132272179	Missense_Mutation	novel	G315S	0.27
SKCM	chr5	132271625	Intron	NA		0.31
SKCM	chr5	132266531	Missense_Mutation	rs371212671	D105N	0.5
SKCM	chr5	132271800	Missense_Mutation	NA	P227L	0.44
SKCM	chr5	132271396	Silent	NA	P200P	0.45
SKCM	chr5	132270993	Missense_Mutation	NA	P136S	0.79
SKCM	chr5	132271574	Intron	novel		0.5
SKCM	chr5	132271337	Missense_Mutation	NA	D181H	0.91
SKCM	chr5	132262687	Missense_Mutation	novel	E58K	0.29
SKCM	chr5	132271359	Missense_Mutation	NA	S188F	0.39
SKCM	chr5	132271456	Silent	NA	A220A	0.28
STAD	chr5	132272273	3'UTR	rs757982030		0.36
STAD	chr5	132272159	Missense_Mutation	NA	A308E	0.41
STAD	chr5	132271850	Missense_Mutation	NA	A244P	0.45
STAD	chr5	132270963	Missense_Mutation	NA	P126S	0.22
STAD	chr5	132271849	Silent	rs768047246	G243G	0.26
STAD	chr5	132272166	Silent	NA	V310V	0.15
STAD	chr5	132271012	Missense_Mutation	rs755408398	R142H	0.1
STAD	chr5	132271708	Intron	novel		0.17
STAD	chr5	132271086	Frame_Shift_Del	NA	*S169Afs50**	0.2
STAD	chr5	132271041	Missense_Mutation	rs368514608	E152K	0.27
UCEC	chr5	132262651	Nonsense_Mutation	novel	G46*	0.27
UCEC	chr5	132272089	Missense_Mutation	rs202040278	G285S	0.29
UCEC	chr5	132271833	Missense_Mutation	NA	T238M	0.26
UCEC	chr5	132271422	Missense_Mutation	novel	G209D	0.34
UCEC	chr5	132271040	Silent	rs182865841	S151S	0.4
UCEC	chr5	132270968	Missense_Mutation	novel	E127D	0.25
UCEC	chr5	132262612	Missense_Mutation	novel	H33Y	0.3
UCEC	chr5	132272167	Missense_Mutation	novel	K311E	0.24
UCEC	chr5	132272321	3'UTR	novel		0.58
UCEC	chr5	132271376	Silent	novel	L194L	0.41
UCEC	chr5	132271456	Silent	NA	A220A	0.44
UCEC	chr5	132271086	Frame_Shift_Del	NA	*S169Afs50**	0.47
UCEC	chr5	132271663	Intron	novel		0.22
UCEC	chr5	132272088	Silent	rs771779039	C284C	0.34
UCEC	chr5	132271086	Frame_Shift_Del	NA	*S169Afs50**	0.4
UCEC	chr5	132262665	Silent	novel	Q50Q	0.36
UCEC	chr5	132271363	Missense_Mutation	novel	E189D	0.4
UCEC	chr5	132270987	Nonsense_Mutation	NA	G134*	0.35
UCEC	chr5	132271397	Missense_Mutation	rs778997358	V201M	0.25
UCEC	chr5	132266542	Silent	novel	I108I	0.5

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
KIRP	DEL	0.0382	0.11554
LAML	DEL	0.0838	1.2971e-07
LUAD	DEL	0.3004	7.4776e-05
LUSC	DEL	0.6467	0.002071
MESO	DEL	0.1494	0.20184
PRAD	AMP	0.0285	0.16448
STAD	DEL	0.2698	2.8835e-08
THCA	AMP	0.0361	0.075436
THCA	DEL	0	0.23456

Survival Analysis

Cancer	P-value	Q-value
STAD	0.036	Kaplan-Meier Survival Analysis
ACC	0.016	Kaplan-Meier Survival Analysis
BRCA	0.0033	Kaplan-Meier Survival Analysis
ESCA	0.014	Kaplan-Meier Survival Analysis
KIRP	0.0093	Kaplan-Meier Survival Analysis
COAD	0.015	Kaplan-Meier Survival Analysis
BLCA	0.02	Kaplan-Meier Survival Analysis
UCEC	0.014	Kaplan-Meier Survival Analysis
GBM	0.0017	Kaplan-Meier Survival Analysis
THCA	0.023	Kaplan-Meier Survival Analysis
UVM	0.00014	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

GWAS

PPI

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742