EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000144791 (Gene tree)
Gene ID: 8994
Gene Symbol: LIMD1
Alias: N
Full Name: LIM domains containing 1
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 130,945 bases
Position: chr3:45,555,394-45,686,338
Accession: 6612
RBP type: non-canonical RBP
Summary: (LIM Domains Containing 1) is a Protein Coding gene. Among its related pathways are Tyrosine Kinases / Adaptors and CDK-mediated phosphorylation and removal of Cdc6. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity. An important paralog of this gene is WTIP.

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
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
ENST00000474665	LIMD1-204	513	-	-	- (aa)	-	-
ENST00000465039	LIMD1-203	676	-	-	- (aa)	-	-
ENST00000273317	LIMD1-201	11331	-	ENSP00000273317	676 (aa)	-	Q9UGP4
ENST00000440097	LIMD1-202	2773	-	ENSP00000394537	620 (aa)	-	C9JRJ5

Gene Model

Click here to download ENSG00000144791's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa04390	Hippo signaling pathway	KEGG
hsa04392	Hippo signaling pathway - multiple species	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000144791	Platelet Function Tests	3.0728000E-006	-

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000144791	rs116425179	3	45557211	G	Monocyte chemoattractant protein-1 levels	27989323	[0.098-0.198] SD units increase	0.1476	EFO_0004749
ENSG00000144791	rs34877991	3	45602156	C	Systolic blood pressure	30578418	[0.12-0.23] mmHg decrease	0.1731	EFO_0006335

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000144791's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000932	P-body	21873635.	IBA	Component
GO:0000932	P-body	20616046.	IDA	Component
GO:0001666	response to hypoxia	21873635.	IBA	Process
GO:0001666	response to hypoxia	22286099.	IDA	Process
GO:0002076	osteoblast development	-	ISS	Process
GO:0003714	transcription corepressor activity	21873635.	IBA	Function
GO:0003714	transcription corepressor activity	-	ISS	Function
GO:0005515	protein binding	15542589.18331720.20303269.20616046.22190034.22286099.	IPI	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005634	nucleus	15542589.18439753.	IDA	Component
GO:0005667	transcription factor complex	21873635.	IBA	Component
GO:0005737	cytoplasm	15542589.18439753.	IDA	Component
GO:0005829	cytosol	-	TAS	Component
GO:0005886	plasma membrane	-	IDA	Component
GO:0005911	cell-cell junction	21873635.	IBA	Component
GO:0005912	adherens junction	21873635.	IBA	Component
GO:0005912	adherens junction	20303269.	IDA	Component
GO:0005925	focal adhesion	18439753.	IDA	Component
GO:0006355	regulation of transcription, DNA-templated	10647888.	TAS	Process
GO:0007010	cytoskeleton organization	21873635.	IBA	Process
GO:0007010	cytoskeleton organization	21834987.	IMP	Process
GO:0007165	signal transduction	10647888.	TAS	Process
GO:0007275	multicellular organism development	10647888.	TAS	Process
GO:0008270	zinc ion binding	10647888.	TAS	Function
GO:0008360	regulation of cell shape	21834987.	IMP	Process
GO:0016310	phosphorylation	18439753.	IDA	Process
GO:0016442	RISC complex	20616046.	IDA	Component
GO:0016477	cell migration	21834987.	IMP	Process
GO:0033962	cytoplasmic mRNA processing body assembly	20616046.	IMP	Process
GO:0035195	gene silencing by miRNA	20616046.	IMP	Process
GO:0035331	negative regulation of hippo signaling	21873635.	IBA	Process
GO:0035331	negative regulation of hippo signaling	20303269.	IDA	Process
GO:0045668	negative regulation of osteoblast differentiation	-	ISS	Process
GO:0045892	negative regulation of transcription, DNA-templated	15542589.	IDA	Process
GO:0045892	negative regulation of transcription, DNA-templated	22286099.	IMP	Process
GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	-	TAS	Process
GO:0090090	negative regulation of canonical Wnt signaling pathway	-	ISS	Process
GO:2000637	positive regulation of gene silencing by miRNA	21873635.	IBA	Process
GO:2000637	positive regulation of gene silencing by miRNA	20616046.	IMP	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
19060205	The chromosome 3p21.3-encoded gene, LIMD1, is a critical tumor suppressor involved in human lung cancer development.	Proc Natl Acad Sci U S A	2008 Dec 16	Sharp TV	doi: 10.1073/pnas.0805003105
18712738	Differential subcellular localisation of the tumour suppressor protein LIMD1 in breast cancer correlates with patient survival.	Int J Cancer	2008 Nov 15	Spendlove I	doi: 10.1002/ijc.23851.
29930174	A HIF-LIMD1 negative feedback mechanism mitigates the pro-tumorigenic effects of hypoxia.	EMBO Mol Med	2018 Aug	Foxler DE	doi: 10.15252/emmm.201708304.
15542589	LIM domains-containing protein 1 (LIMD1), a tumor suppressor encoded at chromosome 3p21.3, binds pRB and represses E2F-driven transcription.	Proc Natl Acad Sci U S A	2004 Nov 23	Sharp TV	-
17889706	Identification of rare variants in the hLIMD1 gene in breast cancer.	Cancer Genet Cytogenet	2007 Oct 1	Huggins CJ	-
29654110	Deregulation of LIMD1-VHL-HIF-1α-VEGF pathway is associated with different stages of cervical cancer.	Biochem J	2018 May 31	Chakraborty C	doi: 10.1042/BCJ20170649.

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr3	45595349	Missense_Mutation	novel	S157F	0.43
BLCA	chr3	45596254	Missense_Mutation	novel	E459Q	0.3
BLCA	chr3	45595120	Frame_Shift_Del	novel	*G81Wfs14**	0.65
BLCA	chr3	45674380	Missense_Mutation	NA	R621T	0.39
BLCA	chr3	45672705	Missense_Mutation	novel	G553W	0.1
BLCA	chr3	45595766	Missense_Mutation	novel	S296F	0.22
BRCA	chr3	45595022	Frame_Shift_Ins	NA	*A49Rfs27**	0.32
CESC	chr3	45595646	Missense_Mutation	NA	S256N	0.25
CESC	chr3	45678261	3'UTR	novel		0.33
CESC	chr3	45595958	Missense_Mutation	NA	S360L	0.32
CESC	chr3	45594909	Silent	rs762773830	E10E	0.11
CESC	chr3	45596162	Missense_Mutation	novel	R428M	0.45
CESC	chr3	45677333	3'UTR	novel		0.35
CESC	chr3	45595938	Silent	rs199819721	S353S	0.72
CESC	chr3	45689089	3'Flank	rs531637941		0.11
CESC	chr3	45674380	Missense_Mutation	NA	R621T	0.33
CESC	chr3	45672698	Silent	NA	Q550Q	0.36
CESC	chr3	45678398	3'UTR	novel		0.34
CHOL	chr3	45595717	Missense_Mutation	novel	L280V	0.73
CHOL	chr3	45678247	3'UTR	novel		0.63
COAD	chr3	45595833	Frame_Shift_Del	NA	*G320Vfs6**	0.25
COAD	chr3	45672777	Missense_Mutation	rs751216668	V577M	0.09
COAD	chr3	45595240	Missense_Mutation	NA	A121T	0.5
COAD	chr3	45595833	Frame_Shift_Del	NA	*G320Vfs6**	0.36
COAD	chr3	45595874	Frame_Shift_Ins	NA	*Q334Pfs65**	0.29
COAD	chr3	45595425	Silent	NA	N182N	0.38
COAD	chr3	45677082	3'UTR	rs752546158		0.3
COAD	chr3	45677127	3'UTR	novel		0.3
COAD	chr3	45596234	Missense_Mutation	novel	L452H	0.09
COAD	chr3	45677121	3'UTR	novel		0.53
COAD	chr3	45595302	Silent	rs754205344	T141T	0.1
COAD	chr3	45595724	Missense_Mutation	novel	N282S	0.37
COAD	chr3	45595331	Missense_Mutation	NA	R151K	0.1
DLBC	chr3	45594887	Missense_Mutation	novel	K3M	0.11
DLBC	chr3	45594964	Missense_Mutation	rs762091224	F29L	0.85
ESCA	chr3	45596263	Missense_Mutation	novel	A462T	0.38
ESCA	chr3	45676959	Missense_Mutation	rs35343448	R644H	0.4
ESCA	chr3	45595938	Silent	novel	S353S	0.08
GBM	chr3	45594925	Missense_Mutation	NA	E16K	0.31
GBM	chr3	45595715	Missense_Mutation	novel	N279S	0.1
GBM	chr3	45595707	Silent	novel	P276P	0.33
GBM	chr3	45676934	Missense_Mutation	novel	E636Q	0.06
GBM	chr3	45596053	Missense_Mutation	novel	V392L	0.36
HNSC	chr3	45595461	Silent	novel	P194P	0.48
KIRC	chr3	45595852	Missense_Mutation	NA	V325L	0.58
KIRP	chr3	45595920	Missense_Mutation	NA	S347R	0.34
KIRP	chr3	45672817	Splice_Site	novel	X590_splice	0.19
LAML	chr3	45596148	Silent	novel	S423S	0.5
LAML	chr3	45677039	Missense_Mutation	novel	L671V	0.49
LGG	chr3	45595446	Silent	novel	K189K	0.1
LIHC	chr3	45677113	3'UTR	novel		0.5
LUAD	chr3	45674386	Missense_Mutation	novel	Y623C	0.19
LUAD	chr3	45595818	Missense_Mutation	novel	R313S	0.06
LUAD	chr3	45665709	Missense_Mutation	novel	D524N	0.13
LUAD	chr3	45673503	Nonsense_Mutation	NA	E608*	0.23
LUAD	chr3	45596028	Silent	NA	L383L	0.13
LUAD	chr3	45636235	Silent	novel	F498F	0.05
LUSC	chr3	45595240	Missense_Mutation	novel	A121S	0.73
LUSC	chr3	45594952	Missense_Mutation	novel	K25E	0.21
LUSC	chr3	45674397	Missense_Mutation	novel	C627R	0.39
LUSC	chr3	45595830	Silent	rs760923679	G317G	0.41
LUSC	chr3	45676985	Frame_Shift_Del	novel	*F653Lfs33**	0.34
OV	chr3	45595363	Missense_Mutation	novel	F162L	0.05
OV	chr3	45676992	Missense_Mutation	novel	H655L	0.05
PAAD	chr3	45595480	Missense_Mutation	novel	G201S	0.17
PAAD	chr3	45595893	Missense_Mutation	novel	Q338H	0.17
PRAD	chr3	45596041	Missense_Mutation	novel	L388F	0.42
PRAD	chr3	45595046	Missense_Mutation	novel	H56P	0.19
PRAD	chr3	45595106	Missense_Mutation	novel	G76D	0.5
PRAD	chr3	45674362	Missense_Mutation	rs776070787	R615H	0.47
READ	chr3	45595602	Silent	NA	E241E	0.32
SKCM	chr3	45668313	Nonsense_Mutation	novel	S533*	0.23
SKCM	chr3	45595916	Missense_Mutation	NA	S346F	0.18
SKCM	chr3	45676928	Frame_Shift_Del	novel	*G634Vfs26**	0.35
SKCM	chr3	45594959	Missense_Mutation	novel	G27V	0.38
SKCM	chr3	45595281	Silent	NA	S134S	0.13
SKCM	chr3	45595578	Silent	novel	S233S	0.53
SKCM	chr3	45595579	Silent	novel	L234L	0.52
SKCM	chr3	45672750	Missense_Mutation	rs776587629	E568K	0.77
SKCM	chr3	45665655	Missense_Mutation	novel	K506E	0.4
STAD	chr3	45595833	Frame_Shift_Del	NA	*G320Vfs6**	0.2
STAD	chr3	45676941	Missense_Mutation	rs140945464	N638S	0.04
STAD	chr3	45596073	Silent	NA	E398E	0.33
STAD	chr3	45595344	Silent	rs374578310	A155A	0.25
STAD	chr3	45636219	Missense_Mutation	novel	Y493S	0.35
STAD	chr3	45595833	Frame_Shift_Del	NA	*G320Vfs6**	0.26
STAD	chr3	45595563	Silent	NA	N228N	0.14
STAD	chr3	45595517	Missense_Mutation	novel	G213V	0.07
STAD	chr3	45595451	Missense_Mutation	NA	G191D	0.4
STAD	chr3	45672714	Missense_Mutation	novel	Y556H	0.26
STAD	chr3	45596000	Missense_Mutation	rs755410946	C374Y	0.21
STAD	chr3	45595644	Silent	NA	S255S	0.19
THCA	chr3	45594913	Missense_Mutation	NA	S12C	0.27
UCEC	chr3	45678277	3'UTR	novel		0.29
UCEC	chr3	45595665	Silent	novel	L262L	0.39
UCEC	chr3	45665665	Frame_Shift_Ins	novel	*A511Sfs12**	0.3
UCEC	chr3	45678235	3'UTR	novel		0.14
UCEC	chr3	45688871	3'Flank	novel		0.59
UCEC	chr3	45595954	Missense_Mutation	NA	G359C	0.33
UCEC	chr3	45676999	Silent	NA	C657C	0.17
UCEC	chr3	45595023	Silent	rs143204461	F48F	0.15
UCEC	chr3	45672791	Missense_Mutation	novel	N581K	0.07
UCEC	chr3	45595567	Nonsense_Mutation	rs770554958	R230*	0.31
UCEC	chr3	45636220	Silent	rs149909565	Y493Y	0.19
UCEC	chr3	45677100	3'UTR	rs758471445		0.25
UCEC	chr3	45688796	3'Flank	novel		0.5
UCEC	chr3	45595094	Missense_Mutation	rs762002629	R72M	0.17
UCEC	chr3	45672740	Silent	NA	V564V	0.28
UCEC	chr3	45677937	3'UTR	novel		0.6
UCEC	chr3	45677287	3'UTR	novel		0.31
UCEC	chr3	45678228	3'UTR	novel		0.38
UCEC	chr3	45674366	Silent	rs761289549	V616V	0.34
UCEC	chr3	45672722	Silent	rs772955390	P558P	0.41
UCEC	chr3	45595480	Missense_Mutation	novel	G201S	0.15
UCEC	chr3	45677337	3'UTR	novel		0.29
UCEC	chr3	45595160	Missense_Mutation	rs773501255	G94D	0.45
UCEC	chr3	45674366	Silent	rs761289549	V616V	0.46
UCEC	chr3	45677236	3'UTR	novel		0.13
UCEC	chr3	45594939	Missense_Mutation	NA	M20I	0.29
UCEC	chr3	45677190	3'UTR	novel		0.44
UCEC	chr3	45676929	Missense_Mutation	novel	G634D	0.09
UCEC	chr3	45677191	3'UTR	novel		0.66
UCEC	chr3	45595631	Missense_Mutation	novel	I251T	0.2
UCEC	chr3	45595662	Silent	novel	G261G	0.26
UCEC	chr3	45596126	Missense_Mutation	novel	S416Y	0.18
UCEC	chr3	45678097	3'UTR	novel		0.4
UCEC	chr3	45636245	Missense_Mutation	NA	A502T	0.27
UCEC	chr3	45677330	3'UTR	novel		0.57
UCEC	chr3	45595849	Missense_Mutation	novel	G324C	0.48
UCEC	chr3	45596039	Missense_Mutation	novel	S387N	0.36
UCEC	chr3	45595030	Missense_Mutation	novel	K51E	0.45

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
CHOL	DEL	0.8056	0.016387
DLBC	DEL	0.125	0.016959
GBM	DEL	0.078	0.056565
LGG	DEL	0.078	0.00089193
LUAD	DEL	0.3353	0.0021265
PAAD	DEL	0.1793	0.030662
SARC	DEL	0.1907	0.0034746
SKCM	DEL	0.1635	0.13887
TGCT	DEL	0.2	0.08422
THYM	DEL	0.0894	0.037527

Survival Analysis

Cancer	P-value	Q-value
THYM	0.0072	Kaplan-Meier Survival Analysis
KIRC	0.04	Kaplan-Meier Survival Analysis
STAD	0.015	Kaplan-Meier Survival Analysis
SARC	0.01	Kaplan-Meier Survival Analysis
HNSC	0.041	Kaplan-Meier Survival Analysis
PRAD	0.024	Kaplan-Meier Survival Analysis
KIRP	0.016	Kaplan-Meier Survival Analysis
BLCA	0.0011	Kaplan-Meier Survival Analysis
READ	0.0042	Kaplan-Meier Survival Analysis
KICH	0.012	Kaplan-Meier Survival Analysis
LGG	0.00012	Kaplan-Meier Survival Analysis
LUAD	0.00084	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742