EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Phenotypes

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000107438 (Gene tree)
Gene ID: 9124
Gene Symbol: PDLIM1
Alias: CLP-36|hCLIM1|CLP36|CLIM1
Full Name: PDZ and LIM domain 1
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Minus strand
Length: 53,581 bases
Position: chr10:95,237,568-95,291,148
Accession: 2067
RBP type: non-canonical RBP
Summary: This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17. [provided by RefSeq, Oct 2012]

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 & HEK293	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 & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
17068759	Identification and analysis of altered alpha1,6-fucosylated glycoproteins associated with hepatocellular carcinoma metastasis.	Proteomics	2006 Nov	Dai Z	-

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000493949	PDLIM1-205	795	-	-	- (aa)	-	-
ENST00000329399	PDLIM1-201	1452	XM_011540330	ENSP00000360305	329 (aa)	XP_011538632	O00151
ENST00000490391	PDLIM1-203	458	-	-	- (aa)	-	-
ENST00000477757	PDLIM1-202	850	-	-	- (aa)	-	-
ENST00000492511	PDLIM1-204	453	-	-	- (aa)	-	-

Gene Model

Click here to download ENSG00000107438's gene model file

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000107438	Body Weight	9.0130000E-005	-
ENSG00000107438	Platelet Function Tests	3.0608000E-005	-
ENSG00000107438	Platelet Function Tests	2.5482400E-005	-
ENSG00000107438	Platelet Function Tests	3.2294900E-005	-
ENSG00000107438	Platelet Function Tests	1.1193000E-006	-
ENSG00000107438	Platelet Function Tests	1.2040000E-006	-

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000107438's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0001666	response to hypoxia	-	IEA	Process
GO:0003713	transcription coactivator activity	-	IEA	Function
GO:0005667	transcription factor complex	-	IEA	Component
GO:0005856	cytoskeleton	-	IEA	Component
GO:0005913	cell-cell adherens junction	25468996.	HDA	Component
GO:0005925	focal adhesion	21423176.	HDA	Component
GO:0006355	regulation of transcription, DNA-templated	-	IEA	Process
GO:0006979	response to oxidative stress	8522188.	TAS	Process
GO:0030018	Z disc	-	IEA	Component
GO:0046872	metal ion binding	-	IEA	Function
GO:0098609	cell-cell adhesion	-	IEA	Process
GO:0098641	cadherin binding involved in cell-cell adhesion	25468996.	HDA	Function
GO:1903508	positive regulation of nucleic acid-templated transcription	-	IEA	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
26119933	Glioma invasion mediated by the p75 neurotrophin receptor (p75(NTR)/CD271) requires regulated interaction with PDLIM1.	Oncogene	2016 Mar 17	Ahn BY	doi: 10.1038/onc.2015.199
24662836	PDZ and LIM domain protein 1(PDLIM1)/CLP36 promotes breast cancer cell migration, invasion and metastasis through interaction with α-actinin.	Oncogene	2015 Mar 5	Liu Z	doi: 10.1038/onc.2014.64
26701804	PDLIM1 Stabilizes the E-Cadherin/β-Catenin Complex to Prevent Epithelial-Mesenchymal Transition and Metastatic Potential of Colorectal Cancer Cells.	Cancer Res	2016 Mar 1	Chen HN	doi: 10.1158/0008-5472.CAN-15-1962
27068564	Autoantibodies against TYMS and PDLIM1 proteins detected as circulatory signatures in Indian breast cancer patients.	Proteomics Clin Appl	2016 May	Gupta P	doi: 10.1002/prca.201500138.

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr10	95263903	Missense_Mutation	novel	S165L	0.38
BLCA	chr10	95264008	Missense_Mutation	novel	S130W	0.17
BRCA	chr10	95238622	Missense_Mutation	rs374874749	S250L	0.15
BRCA	chr10	95247339	Missense_Mutation	NA	S187R	0.38
BRCA	chr10	95268787	Silent	NA	S108S	0.18
CESC	chr10	95290925	5'UTR	rs777091101		0.32
CESC	chr10	95290965	5'UTR	novel		0.67
CESC	chr10	95247329	Missense_Mutation	rs151177027	D191N	0.28
CESC	chr10	95271764	Silent	rs759916547	A39A	0.4
COAD	chr10	95263888	Missense_Mutation	NA	S170N	0.28
COAD	chr10	95247306	Missense_Mutation	NA	K198N	0.37
COAD	chr10	95271739	Missense_Mutation	NA	D48Y	0.35
COAD	chr10	95271746	Silent	NA	C45C	0.34
COAD	chr10	95247329	Missense_Mutation	rs151177027	D191N	0.47
COAD	chr10	95263951	Missense_Mutation	novel	G149D	0.33
COAD	chr10	95264007	Silent	rs764741236	S130S	0.3
COAD	chr10	95263864	Missense_Mutation	novel	P178L	0.19
COAD	chr10	95263967	Missense_Mutation	NA	Y144H	0.41
COAD	chr10	95271692	Missense_Mutation	NA	H63Q	0.34
COAD	chr10	95237930	Frame_Shift_Ins	novel	*K329Qfs7**	0.27
COAD	chr10	95238059	Missense_Mutation	NA	C286R	0.4
COAD	chr10	95237874	3'UTR	novel		0.18
DLBC	chr10	95238682	Missense_Mutation	novel	D230G	0.2
ESCA	chr10	95238649	Missense_Mutation	novel	K241R	0.44
GBM	chr10	95238577	Missense_Mutation	novel	T265N	0.18
GBM	chr10	95271658	Missense_Mutation	novel	D75N	0.23
HNSC	chr10	95290829	Silent	rs775650719	A29A	0.29
HNSC	chr10	95268788	Missense_Mutation	NA	S108F	0.25
KIRC	chr10	95238620	Missense_Mutation	NA	I251F	0.33
KIRP	chr10	95238656	Missense_Mutation	NA	S239R	0.36
LGG	chr10	95237803	3'UTR	novel		0.5
LGG	chr10	95268790	Silent	novel	A107A	0.14
LUAD	chr10	95268778	Missense_Mutation	novel	Q111H	0.13
LUSC	chr10	95247258	Silent	rs762617070	T214T	0.17
LUSC	chr10	95290843	Nonsense_Mutation	novel	E25*	0.42
LUSC	chr10	95247314	Frame_Shift_Del	novel	*V196Ffs11**	0.28
OV	chr10	95247278	Missense_Mutation	NA	E208K	0.14
OV	chr10	95263885	Missense_Mutation	NA	G171V	0.19
READ	chr10	95247270	Silent	rs141682059	P210P	0.5
SKCM	chr10	95263970	Nonsense_Mutation	novel	Q143*	0.33
SKCM	chr10	95247234	Silent	NA	I222I	0.33
SKCM	chr10	95268825	Missense_Mutation	NA	E96K	0.8
SKCM	chr10	95238665	Missense_Mutation	novel	G236R	0.33
SKCM	chr10	95264034	Silent	novel	N121N	0.44
SKCM	chr10	95271675	Missense_Mutation	NA	R69K	0.43
SKCM	chr10	95238616	Missense_Mutation	NA	G252E	0.31
SKCM	chr10	95271715	Missense_Mutation	NA	E56K	0.38
SKCM	chr10	95238622	Missense_Mutation	rs374874749	S250L	0.55
SKCM	chr10	95263937	Missense_Mutation	NA	E154K	0.12
SKCM	chr10	95268820	Silent	NA	G97G	0.4
SKCM	chr10	95271646	Missense_Mutation	NA	L79F	0.43
SKCM	chr10	95247215	Missense_Mutation	NA	G229R	0.14
SKCM	chr10	95238616	Missense_Mutation	NA	G252E	0.23
SKCM	chr10	95247349	Missense_Mutation	NA	P184L	0.38
SKCM	chr10	95268788	Missense_Mutation	NA	S108F	0.09
SKCM	chr10	95237955	Silent	NA	G320G	0.18
SKCM	chr10	95271646	Missense_Mutation	NA	L79I	0.31
STAD	chr10	95290854	Missense_Mutation	NA	G21D	0.28
STAD	chr10	95238013	Missense_Mutation	NA	V301A	0.28
STAD	chr10	95237981	Missense_Mutation	novel	R312W	0.13
STAD	chr10	95271777	Missense_Mutation	novel	P35H	0.2
TGCT	chr10	95238104	Missense_Mutation	novel	F271L	0.48
THCA	chr10	95290934	5'UTR	novel		0.22
UCEC	chr10	95247270	Silent	rs141682059	P210P	0.46
UCEC	chr10	95237966	Missense_Mutation	novel	P317S	0.43
UCEC	chr10	95237959	Missense_Mutation	novel	E319A	0.42
UCEC	chr10	95271636	Missense_Mutation	novel	A82V	0.37
UCEC	chr10	95237730	3'UTR	novel		0.33
UCEC	chr10	95264032	Missense_Mutation	NA	R122Q	0.27
UCEC	chr10	95247270	Silent	rs141682059	P210P	0.39
UCEC	chr10	95237974	Missense_Mutation	rs752319886	R314Q	0.26
UCEC	chr10	95247258	Silent	rs762617070	T214T	0.17
UCEC	chr10	95264032	Missense_Mutation	NA	R122Q	0.54
UCEC	chr10	95237980	Missense_Mutation	novel	R312Q	0.46
UCEC	chr10	95247237	Missense_Mutation	novel	E221D	0.27
UCEC	chr10	95238621	Silent	rs371730712	S250S	0.31
UCEC	chr10	95238625	Missense_Mutation	rs565368926	A249V	0.42
UCEC	chr10	95238053	Missense_Mutation	novel	D288N	0.25
UCEC	chr10	95238080	Missense_Mutation	rs768989089	R279C	0.4
UCEC	chr10	95264012	Missense_Mutation	rs377056135	A129T	0.31
UCEC	chr10	95247270	Silent	rs141682059	P210P	0.13
UCEC	chr10	95238621	Silent	rs371730712	S250S	0.41
UCEC	chr10	95238617	Missense_Mutation	rs766930662	G252R	0.35
UCEC	chr10	95247270	Silent	rs141682059	P210P	0.26
UCEC	chr10	95237755	3'UTR	rs555889125		0.58
UCEC	chr10	95247258	Silent	rs762617070	T214T	0.28
UCEC	chr10	95268815	Missense_Mutation	rs141713061	R99H	0.25
UCEC	chr10	95263863	Splice_Site	rs778264797	X178_splice	0.09
UCEC	chr10	95238625	Missense_Mutation	rs565368926	A249V	0.31

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
ACC	DEL	0.1	0.19593
CHOL	DEL	0.1667	0.048655
COAD	DEL	0.1729	9.4741e-07
MESO	DEL	0.2759	0.00015289
PAAD	DEL	0.1304	0.169
READ	DEL	0.2424	0.014135
THCA	DEL	0.016	0.011063
THYM	DEL	0.0325	0.10563
UCS	DEL	0.3036	0.1218

Survival Analysis

Cancer	P-value	Q-value
THYM	0.03	Kaplan-Meier Survival Analysis
SARC	0.027	Kaplan-Meier Survival Analysis
MESO	0.00026	Kaplan-Meier Survival Analysis
KIRP	0.016	Kaplan-Meier Survival Analysis
CESC	0.017	Kaplan-Meier Survival Analysis
LAML	0.015	Kaplan-Meier Survival Analysis
UCEC	0.00021	Kaplan-Meier Survival Analysis
GBM	0.023	Kaplan-Meier Survival Analysis
LGG	0.0001	Kaplan-Meier Survival Analysis
CHOL	0.033	Kaplan-Meier Survival Analysis
THCA	0.032	Kaplan-Meier Survival Analysis
UVM	0.00015	Kaplan-Meier Survival Analysis
OV	0.013	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Phenotypes

PPI

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742