Tbio LIMS1 LIM and senescent cell antigen-like-containing domain protein 1

Protein Summary

Description

Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation. 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]

Uniprot Accession IDs

• P48059
• B2RAJ4
• B7Z483
• B7Z7R3
• B7Z907
• Q53TE0
• Q9BS44

Gene Name

• LIMS1

Ensembl ID

• ENST00000332345
• ENSP00000331775
• ENSG00000169756
• ENST00000338045
• ENSP00000337598
• ENST00000393310
• ENSP00000376987
• ENST00000409441
• ENSP00000387264
• ENST00000410093
• ENSP00000386926
• ENST00000544547
• ENSP00000437912

Symbol

• PINCH
• PINCH1
• PINCH
• PINCH1
• PINCH-1

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
interacting protein	0.98
transcription factor perturbation	0.96
microRNA	0.93
biological process	0.91
transcription factor	0.85

Protein Classes

PANTHER Classes

Protein / Structural Protein / Lim And Senescent Cell Antigen-like-containing Domain Protein 1

Protein / Cytoskeletal Protein / Actin Family Cytoskeletal Protein / Lim And Senescent Cell Antigen-like-containing Domain Protein 1

DTO Classes

Protein / Cellular Structure / Actin Family Cytoskeletal Protein / Lim And Senescent Cell Antigen-like-containing Domain Protein 1

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 163.13   (req: < 5)

Gene RIFs: 32   (req: <= 3)

Antibodies: 247   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 163.13   (req: >= 5)

Gene RIFs: 32   (req: > 3)

Antibodies: 247   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 15

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

Find Targets by Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (52)

Explore Interacting Targets

1 – 10 of 52

• See Interactions on String-DB

PARVA

Tbio

Novelty:  0.02736601

p_int:  1

Score:  0.996

Data Source:  BioPlex,STRINGDB

PARVB

Tbio

Novelty:  0.03825772

p_int:  0.99999998

p_ni:  1e-8

p_wrong:  1e-8

Score:  0.997

Data Source:  BioPlex,STRINGDB

ILK

Tchem

Family:  Kinase

Novelty:  0.00147344

p_int:  0.999999658

p_ni:  3.42e-7

Score:  0.999

Data Source:  BioPlex,Reactome,STRINGDB

RSU1

Tbio

Novelty:  0.01645054

p_int:  0.999986818

p_ni:  0.000013182

Score:  0.998

Data Source:  BioPlex,Reactome,STRINGDB

PARVG

Tbio

Novelty:  0.08921402

p_int:  0.999962246

p_ni:  0.000037754

Score:  0.951

Data Source:  BioPlex,STRINGDB

CMAS

Tbio

Family:  Enzyme

Novelty:  0.04295627

p_int:  0.998900104

p_ni:  0.001099896

Score:  0.188

Data Source:  BioPlex,STRINGDB

MYO18A

Tbio

Novelty:  0.05058328

p_int:  0.996282476

p_ni:  0.003717524

Score:  0.219

Data Source:  BioPlex,STRINGDB

MYH4

Tbio

Novelty:  0.00556982

p_int:  0.986619105

p_ni:  0.000144174

p_wrong:  0.013236721

Score:  0.294

Data Source:  BioPlex,STRINGDB

RABGAP1

Tbio

Family:  Enzyme

Novelty:  0.14270101

p_int:  0.981258187

p_ni:  0.018741813

Score:  0.15

Data Source:  BioPlex,STRINGDB

TRIP6

Tbio

Novelty:  0.02183202

p_int:  0.971619485

p_ni:  0.028380515

Score:  0.314

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (11)

Reactome (4)

PathwayCommons (2)

WikiPathways (5)

Cell junction organization (R-HSA-446728)

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1 – 4 of 4

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Cell junction organization	88 targets	R-HSA-446728
Reactome	Cell-Cell communication	121 targets	R-HSA-1500931
Reactome	Cell-extracellular matrix interactions	16 targets	R-HSA-446353
Reactome	Regulation of cytoskeletal remodeling and cell spreading by IPP complex components	8 targets	R-HSA-446388

Name	Explore in Pharos	Explore in Source
Cell junction organization	88 targets	R-HSA-446728
Cell-Cell communication	121 targets	R-HSA-1500931
Cell-extracellular matrix interactions	16 targets	R-HSA-446353
Regulation of cytoskeletal remodeling and cell spreading by IPP complex components	8 targets	R-HSA-446388

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (21)

Functions (2)

Components (6)

Processes (13)

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1 – 2 of 2

GO Term	Evidence	Assigned by
zinc ion binding	Inferred from Direct Assay (IDA)	UniProtKB
protein kinase binding	Inferred from Physical Interaction (IPI)	UniProtKB

Disease Associations (null)

No disease associations found

GWAS Traits (7)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 7

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mean platelet volume	EFO_0004584	2	2	2		76.2
low density lipoprotein cholesterol measurement	EFO_0004611	4	4	4		73.7
alkaline phosphatase measurement	EFO_0004533	2	2	1	6.2	71.6
apolipoprotein B measurement	EFO_0004615	1	1	1		42.3
Hirsutism	HP_0001007	1	1	0	1.3	33.1

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 7

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mean platelet volume	EFO_0004584	2		76.2
low density lipoprotein cholesterol measurement	EFO_0004611	4		73.7
alkaline phosphatase measurement	EFO_0004533	1	6.2	71.6
apolipoprotein B measurement	EFO_0004615	1		42.3
Hirsutism	HP_0001007	0	1.3	33.1

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Alternative splicing
Cell junction
Cell membrane
Complete proteome
Direct protein sequencing
LIM domain
Membrane
Metal-binding

GWAS Trait Find Similar Targets

No Header	No Header
alkaline phosphatase measurement
apolipoprotein B measurement
birth weight
Hirsutism
low density lipoprotein cholesterol measurement
mean platelet volume
reticulocyte measurement

MGI Phenotype Find Similar Targets

No Header	No Header
cardiovascular system phenotype
cellular phenotype
embryo phenotype
growth/size/body region phenotype
homeostasis/metabolism phenotype
mortality/aging
muscle phenotype

IDG Resources

No IDG generated resources found

Orthologs (11)

1 – 5 of 11

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	LIM zinc finger domain containing 1		694116
Mouse	LIM and senescent cell antigen-like domains 1	MGI:1195263	110829
Rat	LIM zinc finger domain containing 1	RGD:1560732	499443
Dog	LIM zinc finger domain containing 1		474540
Horse	LIM zinc finger domain containing 1	VGNC:49480	100060267

Species	Name	OMA	EggNOG	Inparanoid
Macaque	LIM zinc finger domain containing 1
Mouse	LIM and senescent cell antigen-like domains 1
Rat	LIM zinc finger domain containing 1
Dog	LIM zinc finger domain containing 1
Horse	LIM zinc finger domain containing 1

Publication Statistics

PubMed Score 163.13

PubMed score by year

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PubTator Score 64.66

PubTator score by year

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Related Publications

Text Mined References (64)

GeneRif Annotations (32)

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PMID	Year	Title