Tbio VIM Vimentin

Protein Summary

Description

Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]

Uniprot Accession IDs

• P08670
• B0YJC2
• D3DRU4
• Q15867
• Q15868
• Q15869
• Q548L2
• Q6LER9
• Q8N850
• Q96ML2
• Q9NTM3

Gene Name

• VIM

Ensembl ID

• ENST00000224237
• ENSP00000224237
• ENSG00000026025
• ENST00000544301
• ENSP00000446007

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological term	1
hub protein	1
interacting protein	1
kinase	1
protein complex	1

Protein Classes

No PANTHER Classes or DTO Classes found

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: 3520.2   (req: < 5)

Gene RIFs: 325   (req: <= 3)

Antibodies: 3179   (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: 3520.2   (req: >= 5)

Gene RIFs: 325   (req: > 3)

Antibodies: 3179   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 23

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

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Show Full Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

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 (244)

Explore Interacting Targets

1 – 10 of 244

• See Interactions on String-DB

NEFM

Tbio

Novelty:  0.00239134

p_int:  0.999999746

p_ni:  2.54e-7

Score:  0.83

Data Source:  BioPlex,STRINGDB

DES

Tbio

Novelty:  0.00651741

p_int:  0.999999562

p_ni:  2e-9

p_wrong:  4.36e-7

Score:  0.987

Data Source:  BioPlex,STRINGDB

NES

Tbio

Novelty:  0.00035379

p_int:  0.999998286

p_ni:  0.00000171

p_wrong:  4e-9

Score:  0.864

Data Source:  BioPlex,STRINGDB

INA

Tbio

Novelty:  0.00708581

p_int:  0.999996709

p_ni:  0.000003291

Score:  0.817

Data Source:  BioPlex,STRINGDB

NEFL

Tbio

Novelty:  0.00049255

p_int:  0.999969372

p_ni:  0.000030628

Score:  0.694

Data Source:  BioPlex,STRINGDB

GFAP

Tbio

Novelty:  0.00020932

p_int:  0.999935914

p_ni:  0.000064086

Score:  0.819

Data Source:  BioPlex,Reactome,STRINGDB

GAN

Tbio

Novelty:  0.01069743

p_int:  0.998092133

p_ni:  0.001907867

Score:  0.906

Data Source:  BioPlex,STRINGDB

SYNC

Tbio

Novelty:  0.04605223

p_int:  0.993061397

p_ni:  0.006938603

Score:  0.779

Data Source:  BioPlex,STRINGDB

RSPRY1

Tdark

Novelty:  0.26883105

p_int:  0.990370232

p_ni:  0.009629768

Score:  0.621

Data Source:  BioPlex,STRINGDB

PRMT8

Tchem

Family:  Epigenetic

Novelty:  0.04213384

p_int:  0.949033937

p_ni:  0.050966063

Score:  0.324

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

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

Pathways (26)

Reactome (11)

KEGG (2)

PathwayCommons (4)

WikiPathways (9)

Apoptosis (R-HSA-109581)

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1 – 5 of 11

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Apoptosis	177 targets	R-HSA-109581
Reactome	Apoptotic cleavage of cellular proteins	38 targets	R-HSA-111465
Reactome	Apoptotic execution phase	52 targets	R-HSA-75153
Reactome	Caspase-mediated cleavage of cytoskeletal proteins	12 targets	R-HSA-264870
Reactome	Cytokine Signaling in Immune system	922 targets	R-HSA-1280215

Name	Explore in Pharos	Explore in Source
Apoptosis	177 targets	R-HSA-109581
Apoptotic cleavage of cellular proteins	38 targets	R-HSA-111465
Apoptotic execution phase	52 targets	R-HSA-75153
Caspase-mediated cleavage of cytoskeletal proteins	12 targets	R-HSA-264870
Cytokine Signaling in Immune system	922 targets	R-HSA-1280215

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (37)

Functions (8)

Components (14)

Processes (15)

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1 – 8 of 8

GO Term	Evidence	Assigned by
double-stranded RNA binding	Inferred from Direct Assay (IDA)	MGI
structural constituent of cytoskeleton	Inferred from Direct Assay (IDA)	UniProtKB
identical protein binding	Inferred from Physical Interaction (IPI)	IntAct
keratin filament binding	Inferred from Physical Interaction (IPI)	AgBase
protein C-terminus binding	Inferred from Physical Interaction (IPI)	UniProtKB
protein domain specific binding	Inferred from Physical Interaction (IPI)	UniProtKB
scaffold protein binding	Inferred from Physical Interaction (IPI)	BHF-UCL
structural constituent of eye lens	Inferred from Electronic Annotation (IEA)	Ensembl

Disease Associations ()

No disease associations found

GWAS Traits (10)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 10

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
total cholesterol measurement	EFO_0004574	3	2	3		78.7
aspartate aminotransferase measurement	EFO_0004736	1	1	0	9.4	73.7
low density lipoprotein cholesterol measurement	EFO_0004611	2	2	2		62
mean corpuscular volume	EFO_0004526	1	1	1		59.6
high density lipoprotein cholesterol measurement	EFO_0004612	1	1	1		46.5

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 10

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
total cholesterol measurement	EFO_0004574	3		78.7
aspartate aminotransferase measurement	EFO_0004736	0	9.4	73.7
low density lipoprotein cholesterol measurement	EFO_0004611	2		62
mean corpuscular volume	EFO_0004526	1		59.6
high density lipoprotein cholesterol measurement	EFO_0004612	1		46.5

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Cataract
Coiled coil
Complete proteome
Cytoplasm
Cytoskeleton
Direct protein sequencing
Disease mutation
Glycoprotein

GWAS Trait Find Similar Targets

No Header	No Header
aspartate aminotransferase measurement
high density lipoprotein cholesterol measurement
homocysteine measurement
low density lipoprotein cholesterol measurement
mean corpuscular volume
platelet count
platelet crit
red blood cell distribution width
total cholesterol measurement
triglyceride measurement

MGI Phenotype Find Similar Targets

No Header	No Header
behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype
immune system phenotype
mortality/aging
muscle phenotype
nervous system phenotype
vision/eye phenotype

IDG Resources

No IDG generated resources found

Orthologs (13)

1 – 5 of 13

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	vimentin	VGNC:5877	493952
Macaque	vimentin		705289
Mouse	vimentin	MGI:98932	22352
Rat	vimentin	RGD:621646	81818
Dog	vimentin	VGNC:48263	477991

Species	Name	OMA	EggNOG	Inparanoid
Chimp	vimentin
Macaque	vimentin
Mouse	vimentin
Rat	vimentin
Dog	vimentin

Publication Statistics

PubMed Score 3520.20

PubMed score by year

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PubTator Score 8543.76

PubTator score by year

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Related Publications

Text Mined References (419)

GeneRif Annotations (325)

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10

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PMID	Year	Title