TISIDB

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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 [ TOP ]
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 [ TOP ]
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 [ TOP ]
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

> KEGG and Reactome Pathway

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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
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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

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Literatures describing the relation between VIM and anti-tumor immunity in human cancer.

PMID	Cancer type	Relation to immunity	Evidence sentences
29721376	Non-Small Cell Lung Carcinoma	Inhibit immunity	Moreover PD-L1 is overexpressed in VIMENTIN positive NSCLC tissues.

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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

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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
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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

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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
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	-0.436	0.208
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	-0.272	0.958
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-0.552	0.881
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	-0.273	0.596
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	-0.599	0.857
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.142	0.974
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.281	0.693
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	-0.366	0.908
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	-0.239	0.947
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.311	0.93
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	0.364	0.946
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	-0.294	0.059

> Mutation difference between responders and non-responders

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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
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	0	1.4	-1.4	1
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	0	1.7	-1.7	1
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	4.8	0	4.8	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	7.7	0	7.7	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0	0	0	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	0	0	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	0	0	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	0	1

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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 [ TOP ]

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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 [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
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 [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of VIM expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between VIM and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	VIM
Name	vimentin
Aliases	CTRCT30; HEL113; epididymis luminal protein 113
Chromosomal Location	10p13
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting VIM collected from DrugBank database.

> Drugs from DrugBank database

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Details on drugs targeting VIM.

ID	Name	Drug Type	Targets	#Targets
DB11638	Artenimol	Small Molecule	ACTG1, ALB, ALDH7A1, ALDOA, ANXA2, ATP5A1, ATP5L, ATP5O, CAST, CCT ......	79
DB12695	Phenethyl Isothiocyanate	Small Molecule	ACTA2, ACTB, ATP5B, ATP5I, ATP5L, CYB5B, DIABLO, FBXO41, HNRNPF, H ......	45

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