Gene Report

Basic Information

Approved Symbol	VIM
Approved Name	vimentin
Location	10p13
Position	chr10:17270258-17279592 (+)
External Links	Entrez Gene: 7431 Ensembl: ENSG00000026025 UCSC: uc001iou.2 HGNC ID: 12692
No. of Studies (Positive/Negative)	1(1/0)
Type	Literature-origin; Protein mapped

Positive relationships between VIM and MDD (count: 1)

Name in Literature	Reference	Research Type	Statistical Result	Relation Description
Vimentin	Tochigi, 2008	patients and normal controls		Genes differentially expressed in major depression Genes differentially expressed in major depression

Positive relationships between VIM and other components at different levels (count: 0)

Positive relationship network of VIM in MK4MDD

Network loading ...

Note:
1. The different color of the nodes denotes the level of the nodes.

Genetic/Epigenetic Locus	Protein and Other Molecule	Cell and Molecular Pathway	Neural System	Cognition and Behavior	Symptoms and Signs	Environment	MDD

2. Besides the component related relationships from literature, gene mapped protein and protein mapped gene are also shown in the network. If the mapped gene or protein is not from literature, square node would be used instead of Circle node. Accordingly, the relationship is marked with dot line.
2. User can drag the nodes to rearrange the layout of the network. Click the node will enter the report page of the node. Right-click will show also the menus to link to the report page of the node and remove the node and related edges. Hover the node will show the level of the node and hover the edge will show the evidence/description of the edge.
3. The network is generated using Cytoscape Web

Negative relationships between VIM and MDD (count: 0)

Negative relationships between VIM and other components at different levels (count: 0)

VIM related SNPs in MK4MDD (count: 0)

VIM related proteins in MK4MDD (count: 1)

Approved Name	UniportKB	No. of Studies (Positive/Negative)	Source
Vimentin	P08670	1(1/0)	Literature-origin

VIM related GO terms (count: 26)

ID	Name	Type	Evidence
Literature-origin GO terms
GO:0006915	apoptotic process	biological process	TAS
GO:0005856	cytoskeleton	cellular component	IDA[16769727]; TAS[16130169]

ID	Name	Type	Evidence
Gene mapped GO terms
GO:0060020	Bergmann glial cell differentiation	biological process	IEA
GO:0005200	structural constituent of cytoskeleton	molecular function	IDA[11889032]
GO:0005886	plasma membrane	cellular component	IDA[19270731]
GO:0005777	peroxisome	cellular component	IDA[17881773]
GO:0019048	virus-host interaction	biological process	IEA
GO:0070062	extracellular vesicular exosome	cellular component	IDA
GO:0005882	intermediate filament	cellular component	IDA[11889032]
GO:0042995	cell projection	cellular component	IEA
GO:0005212	structural constituent of eye lens	molecular function	IEA
GO:0010977	negative regulation of neuron projection development	biological process	IEA
GO:0097110	scaffold protein binding	molecular function	IPI[10852826]
GO:0005737	cytoplasm	cellular component	IDA[9150946]
GO:0014002	astrocyte development	biological process	IEA
GO:0045111	intermediate filament cytoskeleton	cellular component	IDA
GO:0042802	identical protein binding	molecular function	IPI[16169070]
GO:0005515	protein binding	molecular function	IPI
GO:0030049	muscle filament sliding	biological process	TAS
GO:0031252	cell leading edge	cellular component	IEA
GO:0006921	cellular component disassembly involved in execution phase of apoptosis	biological process	TAS
GO:0070307	lens fiber cell development	biological process	IEA
GO:0008022	protein C-terminus binding	molecular function	IPI[19270731]
GO:0045109	intermediate filament organization	biological process	IEA
GO:0005829	cytosol	cellular component	IDA[19270731]; TAS
GO:0006928	cellular component movement	biological process	TAS[16130169]

VIM related KEGG pathways (count: 0)

VIM related BioCarta pathways (count: 0)

VIM related Reactome pathways (count: 6)

ID	Name	Description
Gene mapped Reactome pathways
REACT_995	apoptotic execution_phase	In the execution phase of apoptosis, effector caspases cleav...... In the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucleus and other organelles, DNA fragmentation, chromatin condensation, cell shrinkage and cell detachment and membrane blebbing. More...
REACT_17044	muscle contraction
REACT_578	apoptosis	Apoptosis is a distinct form of cell death that is functiona...... Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of cell-death, and the mechanisms of various apoptotic pathways are still being revealed today. The two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptors The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53. In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes. More...
REACT_107	genes involved_in_apoptotic_cleavage_of_cellular_proteins	Apoptotic cell death is achieved by the caspase-mediated cle...... Apoptotic cell death is achieved by the caspase-mediated cleavage of various vital proteins. Among caspase targets are proteins such as E-cadherin, Beta-catenin, alpha fodrin, GAS2, FADK, alpha adducin, HIP-55, and desmoglein involved in cell adhesion and maintenance of the cytoskeletal architecture. Cleavage of proteins such as APC and CIAP1 can further stimulate apoptosis by produce proapoptotic proteins. More...
REACT_16969	striated muscle_contraction	Striated muscle contraction is a process whereby force is ge...... Striated muscle contraction is a process whereby force is generated within striated muscle tissue, resulting in a change in muscle geometry, or in short, increased force being exerted on the tendons. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle composed of myofibrils, containing repeating units called sarcomeres, in which the contractile myofibrils are arranged in parallel to the axis of the cell, resulting in transverse or oblique striations observable at the level of the light microscope. Here striated muscle contraction is represented on the basis of calcium binding to the troponin complex, which exposes the active sites of actin. Once the active sites of actin are exposed, the myosin complex bound to ADP can bind actin and the myosin head can pivot, pulling the thin actin and thick myosin filaments past one another. Once the myosin head pivots, ADP is ejected, a fresh ATP can be bound and the energy from the hydrolysis of ATP to ADP is channeled into kinetic energy by resetting the myosin head. With repeated rounds of this cycle the sarcomere containing the thin and thick filaments effectively shortens, forming the basis of muscle contraction. More...
REACT_13541	caspase mediated_cleavage_of_cytoskeletal_proteins	Caspase-mediated cleavage of a number of proteins in the cor...... Caspase-mediated cleavage of a number of proteins in the cortical actin network ( ) microfilament system and others involved in maintenance of the cytoskeletal architecture (vimentin, or Gas2 and plectin) may directly contribute to apoptotic changes in cell shape. More...

VIM related interactors from protein-protein interaction data in HPRD (count: 113)

Gene	Interactor	Interactor in MK4MDD?	Experiment Type	PMID
VIM	CASP6	No	in vitro;in vivo	11514563 , 11423904 , 10469173
VIM	BFSP1	No	in vitro;in vivo	1478967 , 1918147
VIM	SIRT6	No	yeast 2-hybrid	16169070
VIM	ZNF384	No	in vivo;yeast 2-hybrid	16510139
VIM	PSME1	No	yeast 2-hybrid	16169070
VIM	HABP4	No	yeast 2-hybrid	16169070
VIM	NFATC2	No	yeast 2-hybrid	16169070
VIM	NEFL	No	in vitro;yeast 2-hybrid	15383276
VIM	COPS6	No	yeast 2-hybrid	15383276
VIM	FABP4	No	yeast 2-hybrid	16169070
VIM	YWHAZ	No	in vivo	10887173
VIM	CAMK2D	No	in vitro	10852918 , 15345747
VIM	SERBP1	No	yeast 2-hybrid	16169070
VIM	FUBP1	No	yeast 2-hybrid	16169070
VIM	DSP	No	in vitro;yeast 2-hybrid	9261168
VIM	MEN1	No	in vitro;in vivo	12169273
VIM	SH3GL3	No	yeast 2-hybrid	15383276
VIM	CRCT1	No	yeast 2-hybrid	16169070
VIM	CAPN1	No	yeast 2-hybrid	12358155
VIM	SRRT	No	yeast 2-hybrid	16169070
VIM	DIS3L2	No	yeast 2-hybrid	16169070
VIM	RAD51	No	yeast 2-hybrid	16169070
VIM	SUMO2	No	yeast 2-hybrid	16169070
VIM	KRT20	No	yeast 2-hybrid	16189514
VIM	ALS2CR11	No	yeast 2-hybrid	16189514
VIM	LOR	No	yeast 2-hybrid	16169070
VIM	SETDB1	Yes	yeast 2-hybrid	15383276
VIM	PSMD7	No	yeast 2-hybrid	15383276
VIM	PIAS4	No	yeast 2-hybrid	15383276
VIM	GOPC	No	yeast 2-hybrid	16189514
VIM	RAB8B	Yes	in vivo	12639940
VIM	C7orf64	No	yeast 2-hybrid	15383276
VIM	ABLIM1	No	yeast 2-hybrid	16189514
VIM	CRMP1	No	in vivo	15383276
VIM	CASP9	No	in vitro;in vivo	11514563 , 11423904 , 10469173
VIM	PKN1	No	in vitro;yeast 2-hybrid	9175763
VIM	IVNS1ABP	No	yeast 2-hybrid	16169070
VIM	CHD3	No	yeast 2-hybrid	15383276
VIM	SH3YL1	No	yeast 2-hybrid	16169070
VIM	CDK1	No	in vitro	7983050 , 15345747
VIM	BHLHE40	No	yeast 2-hybrid	16169070
VIM	MYST2	No	yeast 2-hybrid	15383276
VIM	MICAL1	No	in vitro	11827972
VIM	HMG20B	No	yeast 2-hybrid	16169070
VIM	STX1A	Yes	yeast 2-hybrid	16169070
VIM	ING5	No	yeast 2-hybrid	15383276
VIM	PLEC1	No	in vitro	3027087
VIM	PPHLN1	No	yeast 2-hybrid	15383276
VIM	DEFB1	No	yeast 2-hybrid	15383276
VIM	VIM	Yes	in vitro;in vivo	12226091 , 11889032 , 11243787 , 11278417
VIM	PAK2	No	in vitro	11895474 , 2500966
VIM	C7orf36	No	yeast 2-hybrid	16169070
VIM	CDH5	No	in vivo	12003790
VIM	WBP11	No	in vivo	11375989
VIM	KIAA1377	No	yeast 2-hybrid	15383276
VIM	ATN1	No	yeast 2-hybrid	16169070
VIM	ROCK1	No	in vitro;in vivo	9565595
VIM	CREB1	Yes	yeast 2-hybrid	16169070
VIM	CASP3	No	in vitro;in vivo	10469173 , 11423904 , 11514563
VIM	MRPL44	No	yeast 2-hybrid	16169070
VIM	NUP85	No	in vivo	12706117
VIM	BRD1	No	yeast 2-hybrid	16169070
VIM	UPP2	No	in vitro;in vivo	11278417
VIM	PRKACA	No	in vitro	2500966 , 11895474
VIM	ARMCX2	No	yeast 2-hybrid	15383276
VIM	PUF60	No	yeast 2-hybrid	16169070
VIM	SDCCAG3	No	yeast 2-hybrid	16169070
VIM	MAFG	No	yeast 2-hybrid	16169070
VIM	PDLIM1	No	yeast 2-hybrid	16189514
VIM	FAM107A	No	yeast 2-hybrid	16189514
VIM	PKP1	No	in vitro	10852826
VIM	MAN2A2	No	yeast 2-hybrid	16169070
VIM	OSBP2	No	in vitro	11802775
VIM	TCHP	No	yeast 2-hybrid	16189514
VIM	TNFRSF14	No	yeast 2-hybrid	16169070
VIM	DPPA4	No	yeast 2-hybrid	16169070
VIM	XRCC4	No	yeast 2-hybrid	16169070
VIM	UPP1	No	in vitro;in vivo	11278417
VIM	APIP	No	yeast 2-hybrid	16189514
VIM	RABAC1	No	yeast 2-hybrid	16169070
VIM	ZHX1	No	yeast 2-hybrid	15383276
VIM	HAP1	No	yeast 2-hybrid	15383276
VIM	CASP7	No	in vitro	10469173 , 11423904 , 11514563
VIM	SYN1	Yes	yeast 2-hybrid	16169070
VIM	TRIM28	No	yeast 2-hybrid	16169070
VIM	PPL	No	yeast 2-hybrid	12366696
VIM	SMAD3	No	in vitro	15527767
VIM	TRIM29	No	in vitro;yeast 2-hybrid	7644499
VIM	PLA2G4A	No	in vitro	10625659
VIM	RIBC2	No	yeast 2-hybrid	16189514
VIM	NME2	No	in vivo	11082283
VIM	TRIOBP	No	yeast 2-hybrid	16169070
VIM	SLC27A6	No	yeast 2-hybrid	16169070
VIM	ITGB4	No	in vivo	12441134
VIM	PKD1	No	in vitro;in vivo;yeast 2-hybrid	11581269
VIM	GFAP	Yes	yeast 2-hybrid	16189514
VIM	DNM1L	No	in vitro;yeast 2-hybrid	15383276
VIM	SLC25A6	No	yeast 2-hybrid	16169070
VIM	SUMO3	No	yeast 2-hybrid	16169070
VIM	NOC4L	No	yeast 2-hybrid	16189514
VIM	NIF3L1	No	yeast 2-hybrid	16189514
VIM	C1orf103	No	yeast 2-hybrid	16169070
VIM	UTP14A	No	yeast 2-hybrid	15383276
VIM	CASP8	No	in vivo	11423904 , 10469173
VIM	YWHAE	Yes	in vitro;in vivo	10887173
VIM	TUBGCP4	No	yeast 2-hybrid	16189514
VIM	DCTN1	No	in vivo	14600259
VIM	KIAA0408	No	yeast 2-hybrid	16189514
VIM	SVIL	No	VV	12202484
VIM	TTR	Yes	yeast 2-hybrid	16169070
VIM	DYNLL1	No	in vitro	14760703
VIM	KIF15	No	yeast 2-hybrid	16169070
VIM	PSMA1	No	yeast 2-hybrid	16189514

Gene Report

Literature-origin GO terms

Gene mapped GO terms

Gene mapped Reactome pathways