Browse VIM

Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Cytoplasm Cytoplasm, cytoskeleton Nucleus matrix
Domain PF00038 Intermediate filament protein
PF04732 Intermediate filament head (DNA binding) region
Function

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. ; FUNCTION: Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

> Gene Ontology
 
Biological Process GO:0001654 eye development
GO:0002064 epithelial cell development
GO:0002088 lens development in camera-type eye
GO:0003012 muscle system process
GO:0006936 muscle contraction
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0007423 sensory organ development
GO:0010001 glial cell differentiation
GO:0010721 negative regulation of cell development
GO:0010975 regulation of neuron projection development
GO:0010977 negative regulation of neuron projection development
GO:0014002 astrocyte development
GO:0021782 glial cell development
GO:0030048 actin filament-based movement
GO:0030049 muscle filament sliding
GO:0031345 negative regulation of cell projection organization
GO:0033275 actin-myosin filament sliding
GO:0042063 gliogenesis
GO:0043010 camera-type eye development
GO:0045103 intermediate filament-based process
GO:0045104 intermediate filament cytoskeleton organization
GO:0045109 intermediate filament organization
GO:0045665 negative regulation of neuron differentiation
GO:0048708 astrocyte differentiation
GO:0050768 negative regulation of neurogenesis
GO:0051961 negative regulation of nervous system development
GO:0060020 Bergmann glial cell differentiation
GO:0060395 SMAD protein signal transduction
GO:0070252 actin-mediated cell contraction
GO:0070306 lens fiber cell differentiation
GO:0070307 lens fiber cell development
Molecular Function GO:0001948 glycoprotein binding
GO:0003725 double-stranded RNA binding
GO:0005200 structural constituent of cytoskeleton
GO:0005212 structural constituent of eye lens
GO:0008022 protein C-terminus binding
GO:0019215 intermediate filament binding
GO:0097110 scaffold protein binding
GO:1990254 keratin filament binding
Cellular Component GO:0005777 peroxisome
GO:0005882 intermediate filament
GO:0005924 cell-substrate adherens junction
GO:0005925 focal adhesion
GO:0030055 cell-substrate junction
GO:0031252 cell leading edge
GO:0042579 microbody
GO:0045111 intermediate filament cytoskeleton
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-109581: Apoptosis
R-HSA-111465: Apoptotic cleavage of cellular proteins
R-HSA-75153: Apoptotic execution phase
R-HSA-264870: Caspase-mediated cleavage of cytoskeletal proteins
R-HSA-1280215: Cytokine Signaling in Immune system
R-HSA-168256: Immune System
R-HSA-6785807: Interleukin-4 and 13 signaling
R-HSA-397014: Muscle contraction
R-HSA-5357801: Programmed Cell Death
R-HSA-449147: Signaling by Interleukins
R-HSA-390522: Striated Muscle Contraction
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between VIM and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 
  Literatures describing the relation between VIM and anti-tumor immunity in human cancer.
PMID Cancer type Relation to immunity Evidence sentences
29721376Non-Small Cell Lung CarcinomaInhibit immunityMoreover PD-L1 is overexpressed in VIMENTIN positive NSCLC tissues.
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of VIM in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of VIM in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.4360.208
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-0.2720.958
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.5520.881
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.2730.596
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.5990.857
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.1420.974
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.2810.693
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.3660.908
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-0.2390.947
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.3110.93
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.3640.946
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.2940.059
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of VIM in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277301.4-1.41
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275901.7-1.71
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21174.804.81
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13117.707.71
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of VIM. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of VIM. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by VIM.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of VIM. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of VIM expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between VIM and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolVIM
Namevimentin
Aliases CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location10p13
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting VIM collected from DrugBank database.
> Drugs from DrugBank database
 

  Details on drugs targeting VIM.
ID Name Drug Type Targets #Targets
DB11638ArtenimolSmall MoleculeACTG1, ALB, ALDH7A1, ALDOA, ANXA2, ATP5A1, ATP5L, ATP5O, CAST, CCT ......79
DB12695Phenethyl IsothiocyanateSmall MoleculeACTA2, ACTB, ATP5B, ATP5I, ATP5L, CYB5B, DIABLO, FBXO41, HNRNPF, H ......45