EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
20714146	PINCH protein expression in normal endometrium, atypical endometrial hyperplasia and endometrioid endometrial carcinoma.	Chemotherapy	2010	Zhang HZ	doi: 10.1159/000319953
18957717	PINCH expression and its significance in esophageal squamous cell carcinoma.	Dis Markers	2008	Zhu Z	-
23970013	PINCH expression in relation to radiation response in co-cultured colon cancer cells and in rectal cancer patients.	Oncol Rep	2013 Nov	Holmqvist A	doi: 10.3892/or.2013.2673
25647720	Ras suppressor-1 promotes apoptosis in breast cancer cells by inhibiting PINCH-1 and activating p53-upregulated-modulator of apoptosis (PUMA); verification from metastatic breast cancer human samples.	Clin Exp Metastasis	2015 Mar	Giotopoulou N	doi: 10.1007/s10585-015-9701-x
29079319	Knockdown of PINCH-1 protein sensitizes the estrogen positive breast cancer cells to chemotherapy induced apoptosis.	Pathol Res Pract	2018 Feb	Bhatia A	doi: 10.1016/j.prp.2017.09.026

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr2	108684094	3'UTR	novel		0.56
BLCA	chr2	108655171	Intron	novel		0.26
BLCA	chr2	108675990	Missense_Mutation	NA	R203G	0.63
BLCA	chr2	108683981	Silent	novel	E320E	0.08
BLCA	chr2	108684028	3'UTR	novel		0.21
BLCA	chr2	108672445	Frame_Shift_Ins	novel	*H116Tfs8**	0.14
BLCA	chr2	108678009	Missense_Mutation	rs770508766	R257C	0.66
BLCA	chr2	108683989	Missense_Mutation	rs748854260	G323E	0.14
BRCA	chr2	108683962	Missense_Mutation	NA	R314I	0.22
BRCA	chr2	108659716	Silent	rs144584482	F36F	0.34
BRCA	chr2	108659677	Silent	rs375236817	I23I	0.18
BRCA	chr2	108672388	Missense_Mutation	novel	R96L	0.31
CESC	chr2	108676805	Intron	novel		0.49
CESC	chr2	108621421	Intron	rs149119038		0.25
CESC	chr2	108675953	Silent	novel	V190V	0.42
CESC	chr2	108676603	Splice_Region	novel		0.14
CESC	chr2	108659669	Missense_Mutation	NA	E21K	0.11
COAD	chr2	108659666	Missense_Mutation	rs142167178	A20T	0.26
COAD	chr2	108684054	3'UTR	novel		0.32
COAD	chr2	108684129	3'UTR	novel		0.22
COAD	chr2	108684238	3'Flank	novel		0.12
COAD	chr2	108607235	Intron	novel		0.24
COAD	chr2	108684015	3'UTR	novel		0.1
COAD	chr2	108655029	Intron	novel		0.32
COAD	chr2	108676648	Missense_Mutation	NA	R230C	0.31
COAD	chr2	108676666	Nonsense_Mutation	novel	*G236delinsVDS**	0.04
COAD	chr2	108680723	Silent	NA	C272C	0.08
COAD	chr2	108659642	Missense_Mutation	rs200004487	R12C	0.19
DLBC	chr2	108659630	Missense_Mutation	rs375431434	A8T	0.1
ESCA	chr2	108672414	Missense_Mutation	novel	A105T	0.41
ESCA	chr2	108655006	Intron	novel		0.23
GBM	chr2	108675992	Silent	rs111779374	R203R	0.59
HNSC	chr2	108659747	Missense_Mutation	rs768178569	E47K	0.2
KIRC	chr2	108680708	Frame_Shift_Ins	novel	*N268Kfs2**	0.2
KIRP	chr2	108675983	Silent	rs758889895	I200I	0.44
KIRP	chr2	108684058	3'UTR	novel		0.41
LGG	chr2	108659642	Missense_Mutation	rs200004487	R12C	0.27
LUAD	chr2	108675992	Silent	rs111779374	R203R	0.16
LUSC	chr2	108659750	Missense_Mutation	rs773956158	G48R	0.17
LUSC	chr2	108659751	Missense_Mutation	rs761280581	G48E	0.17
LUSC	chr2	108655104	Intron	novel		0.3
LUSC	chr2	108659758	Silent	NA	F50F	0.14
OV	chr2	108659668	Silent	novel	A20A	0.12
OV	chr2	108659669	Nonsense_Mutation	novel	E21*	0.12
PRAD	chr2	108675992	Silent	rs111779374	R203R	0.4
READ	chr2	108654913	Intron	novel		0.36
READ	chr2	108684020	3'UTR	novel		0.36
SKCM	chr2	108655042	Intron	rs758912054		0.34
SKCM	chr2	108673012	Silent	novel	F159F	0.31
SKCM	chr2	108683943	Missense_Mutation	novel	P308S	0.37
STAD	chr2	108659698	Silent	novel	L30L	0.1
STAD	chr2	108678017	Missense_Mutation	novel	I259M	0.42
STAD	chr2	108675895	Missense_Mutation	NA	D171G	0.08
STAD	chr2	108659660	Missense_Mutation	novel	A18S	0.09
THCA	chr2	108675943	Missense_Mutation	rs767129546	K187R	0.07
UCEC	chr2	108675877	Splice_Site	novel	X165_splice	0.3
UCEC	chr2	108678028	Splice_Site	NA	X263_splice	0.4
UCEC	chr2	108670820	Missense_Mutation	novel	L66F	0.18
UCEC	chr2	108672367	Missense_Mutation	novel	S89I	0.19
UCEC	chr2	108680723	Silent	NA	C272C	0.33
UCEC	chr2	108659716	Silent	rs144584482	F36F	0.27
UCEC	chr2	108655009	Intron	novel		0.32
UCEC	chr2	108675991	Missense_Mutation	rs377342624	R203H	0.37
UCEC	chr2	108676649	Missense_Mutation	NA	R230H	0.77
UCEC	chr2	108672905	Missense_Mutation	novel	R124C	0.63
UCEC	chr2	108673027	Splice_Region	rs779262048	C164C	0.62
UCEC	chr2	108683965	Missense_Mutation	novel	L315R	0.36
UCEC	chr2	108655094	Intron	novel		0.53
UCEC	chr2	108659640	Missense_Mutation	NA	E11G	0.23
UCEC	chr2	108672905	Missense_Mutation	novel	R124C	0.38
UCEC	chr2	108670798	Nonsense_Mutation	novel	Y58*	0.49
UCEC	chr2	108621294	Intron	novel		0.38
UCEC	chr2	108655127	Intron	NA		0.38
UCEC	chr2	108675901	Missense_Mutation	novel	R173L	0.34
UCEC	chr2	108684027	3'UTR	rs778519132		0.45
UCEC	chr2	108659716	Silent	rs144584482	F36F	0.07
UCEC	chr2	108672967	Missense_Mutation	NA	E144D	0.27
UVM	chr2	108680747	Silent	novel	T280T	0.34

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
ACC	DEL	0.1778	0.15279
PAAD	DEL	0.0326	0.2014

Survival Analysis

Cancer	P-value	Q-value
THYM	0.014	Kaplan-Meier Survival Analysis
UCS	0.0096	Kaplan-Meier Survival Analysis
HNSC	0.025	Kaplan-Meier Survival Analysis
SKCM	0.001	Kaplan-Meier Survival Analysis
TGCT	0.047	Kaplan-Meier Survival Analysis
KIRP	0.00028	Kaplan-Meier Survival Analysis
PAAD	0.011	Kaplan-Meier Survival Analysis
CESC	0.032	Kaplan-Meier Survival Analysis
LAML	0.012	Kaplan-Meier Survival Analysis
KICH	0.033	Kaplan-Meier Survival Analysis
UCEC	0.037	Kaplan-Meier Survival Analysis
LIHC	0.0027	Kaplan-Meier Survival Analysis
LGG	0.0001	Kaplan-Meier Survival Analysis
THCA	0.04	Kaplan-Meier Survival Analysis
OV	0.035	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Expression

Transcripts

Gene Model

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000169756 (Gene tree)
Gene ID: 3987
Gene Symbol: LIMS1
Alias: PINCH|PINCH1
Full Name: LIM zinc finger domain containing 1
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 152,892 bases
Position: chr2:108,534,355-108,687,246
Accession: 6616
RBP type: non-canonical RBP
Summary: The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

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
ENST00000422797	LIMS1-207	1544	-	ENSP00000402322	100 (aa)	-	F8WE10
ENST00000338045	LIMS1-202	1876	XM_005263946	ENSP00000337598	387 (aa)	XP_005264003	P48059
ENST00000449684	LIMS1-210	492	-	-	- (aa)	-	-
ENST00000462817	LIMS1-211	566	-	-	- (aa)	-	-
ENST00000434274	LIMS1-209	779	-	ENSP00000410751	55 (aa)	-	F8WB59
ENST00000393310	LIMS1-203	4392	XM_005263951	ENSP00000376987	325 (aa)	XP_005264008	P48059
ENST00000414829	LIMS1-206	439	XM_017004096	ENSP00000399267	117 (aa)	XP_016859585	F8WC86
ENST00000410093	LIMS1-205	1526	-	ENSP00000386926	329 (aa)	-	P48059
ENST00000332345	LIMS1-201	1235	XM_005263950	ENSP00000331775	325 (aa)	XP_005264007	P48059
ENST00000428064	LIMS1-208	637	-	ENSP00000390862	176 (aa)	-	C9JF46
ENST00000409441	LIMS1-204	1627	XM_005263948	ENSP00000387264	362 (aa)	XP_005264005	P48059
ENST00000474038	LIMS1-212	679	-	-	- (aa)	-	-
ENST00000542845	LIMS1-214	727	-	ENSP00000446121	209 (aa)	-	A0A0M3HER1
ENST00000544547	LIMS1-215	4461	XM_005263949	ENSP00000437912	337 (aa)	XP_005264006	P48059
ENST00000496653	LIMS1-213	626	-	-	- (aa)	-	-

Gene Model

Click here to download ENSG00000169756's gene model file

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000169756	rs6542772	2	108558159	C	Excessive hairiness	29895819	[1.17-1.37]	1.27	HP_0001007
ENSG00000169756	rs111995966	2	108558513	G	Monocyte chemoattractant protein-1 levels	27989323	[0.084-0.206] SD units decrease	0.1452	EFO_0004749
ENSG00000169756	rs1866188	2	108640696	A	Eyebrow thickness	30248107			EFO_0007823
ENSG00000169756	rs826681	2	108615619	C	Low density lipoprotein cholesterol levels	29507422	unit decrease	0.025	EFO_0004611
ENSG00000169756	rs826681	2	108615619	C	Total cholesterol levels	29507422	unit decrease	0.025	EFO_0004574

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000169756's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0001837	epithelial to mesenchymal transition	20926685.	IMP	Process
GO:0005515	protein binding	10574708.12432066.15721255.18339839.19074270.20926685.21390327.23088713.23414517.23455922.23877428.25416956.25852190.	IPI	Function
GO:0005829	cytosol	-	TAS	Component
GO:0005886	plasma membrane	-	IEA	Component
GO:0005911	cell-cell junction	20926685.	IMP	Component
GO:0005925	focal adhesion	21423176.	HDA	Component
GO:0005925	focal adhesion	20926685.21390327.	IDA	Component
GO:0005925	focal adhesion	19117955.	IDA	Component
GO:0007569	cell aging	7517666.	TAS	Process
GO:0008270	zinc ion binding	19074270.	IDA	Function
GO:0010628	positive regulation of gene expression	20926685.	IMP	Process
GO:0010811	positive regulation of cell-substrate adhesion	20926685.	IMP	Process
GO:0019901	protein kinase binding	20926685.	IPI	Function
GO:0032991	protein-containing complex	-	IEA	Component
GO:0033209	tumor necrosis factor-mediated signaling pathway	21343177.	IMP	Process
GO:0034329	cell junction assembly	-	TAS	Process
GO:0043547	positive regulation of GTPase activity	20926685.	IMP	Process
GO:0045184	establishment of protein localization	20926685.	IMP	Process
GO:0045892	negative regulation of transcription, DNA-templated	21390327.	IDA	Process
GO:0048471	perinuclear region of cytoplasm	21390327.	IDA	Component
GO:0050678	regulation of epithelial cell proliferation	20926685.	IMP	Process
GO:0051291	protein heterooligomerization	-	IEA	Process
GO:0051894	positive regulation of focal adhesion assembly	20926685.	IMP	Process
GO:0071560	cellular response to transforming growth factor beta stimulus	21390327.	IEP	Process
GO:1900026	positive regulation of substrate adhesion-dependent cell spreading	20926685.	IMP	Process
GO:1901224	positive regulation of NIK/NF-kappaB signaling	21343177.	IMP	Process

EuRBPDB

Note: to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Expression

Transcripts

Gene Model

GWAS

PPI

Gene Ontology

Note: Click here to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Note: to get the extension of tumor abbreviations.