HCSGD entry for VIM
1. General information
| Official gene symbol | VIM |
|---|---|
| Entrez ID | 7431 |
| Gene full name | vimentin |
| Other gene symbols | |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
This gene isn't in PPI subnetwork.
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0003725 | Double-stranded RNA binding | IDA | molecular_function |
| GO:0005198 | Structural molecule activity | IEA | molecular_function |
| GO:0005200 | Structural constituent of cytoskeleton | IDA | molecular_function |
| GO:0005212 | Structural constituent of eye lens | IEA | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005737 | Cytoplasm | IDA | cellular_component |
| GO:0005777 | Peroxisome | IDA | cellular_component |
| GO:0005829 | Cytosol | IDA TAS | cellular_component |
| GO:0005856 | Cytoskeleton | IDA TAS | cellular_component |
| GO:0005882 | Intermediate filament | IDA IEA | cellular_component |
| GO:0005886 | Plasma membrane | IDA | cellular_component |
| GO:0006915 | Apoptotic process | TAS | biological_process |
| GO:0006921 | Cellular component disassembly involved in execution phase of apoptosis | TAS | biological_process |
| GO:0006928 | Cellular component movement | TAS | biological_process |
| GO:0008022 | Protein C-terminus binding | IPI | molecular_function |
| GO:0010977 | Negative regulation of neuron projection development | IEA | biological_process |
| GO:0014002 | Astrocyte development | IEA | biological_process |
| GO:0016032 | Viral process | IEA | biological_process |
| GO:0030049 | Muscle filament sliding | TAS | biological_process |
| GO:0031252 | Cell leading edge | IEA | cellular_component |
| GO:0042802 | Identical protein binding | IPI | molecular_function |
| GO:0042995 | Cell projection | IEA | cellular_component |
| GO:0045109 | Intermediate filament organization | IEA | biological_process |
| GO:0045111 | Intermediate filament cytoskeleton | IDA | cellular_component |
| GO:0060020 | Bergmann glial cell differentiation | IEA | biological_process |
| GO:0070062 | Extracellular vesicular exosome | IDA | cellular_component |
| GO:0070307 | Lens fiber cell development | IEA | biological_process |
| GO:0097110 | Scaffold protein binding | IPI | molecular_function |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.9173110976 | 0.0982717146 | 0.9999902473 | 0.5991147290 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Down | -0.2264713234 |
| GSE13712_SHEAR | Up | 0.1112211344 |
| GSE13712_STATIC | Up | 0.1478884261 |
| GSE19018 | Down | -0.6112900929 |
| GSE19899_A1 | Up | 0.0209025490 |
| GSE19899_A2 | Down | -0.5783618681 |
| PubMed_21979375_A1 | Down | -0.1348449836 |
| PubMed_21979375_A2 | Up | 0.3054616825 |
| GSE35957 | Down | -0.6861940571 |
| GSE36640 | Up | 0.1041653491 |
| GSE54402 | Up | 0.0616262794 |
| GSE9593 | Down | -0.2687465496 |
| GSE43922 | Down | -0.0527348827 |
| GSE24585 | Down | -0.1496286329 |
| GSE37065 | Down | -0.1310358866 |
| GSE28863_A1 | Up | 0.0236242271 |
| GSE28863_A2 | Down | -0.2111821189 |
| GSE28863_A3 | Down | -0.0868846392 |
| GSE28863_A4 | Up | 0.1637425502 |
| GSE48662 | Down | -0.0276411173 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
Not regulated by compounds
- Drugs
Not regulated by drugs
- MicroRNAs
- mirTarBase
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-124-3p | MIMAT0000422 | MIRT004724 | Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 19843643 |
| hsa-miR-124-3p | MIMAT0000422 | MIRT004724 | Proteomics;Microarray | Functional MTI (Weak) | 18668037 |
| hsa-miR-17-3p | MIMAT0000071 | MIRT005028 | qRT-PCR//Western blot | Functional MTI | 19771525 |
| hsa-miR-17-3p | MIMAT0000071 | MIRT005028 | Luciferase reporter assay | Functional MTI | 23418359 |
| hsa-miR-17-3p | MIMAT0000071 | MIRT005028 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-30c-5p | MIMAT0000244 | MIRT007202 | Luciferase reporter assay | Functional MTI | 23224145 |
| hsa-miR-9-5p | MIMAT0000441 | MIRT021395 | Western blot | Non-Functional MTI | 20173740 |
| hsa-miR-138-5p | MIMAT0000430 | MIRT021692 | Reporter assay;Western blot;qRT-PCR;Other | Functional MTI | 21770894 |
| hsa-miR-30a-5p | MIMAT0000087 | MIRT028543 | Proteomics | Functional MTI (Weak) | 18668040 |
| hsa-miR-26b-5p | MIMAT0000083 | MIRT029436 | Microarray | Functional MTI (Weak) | 19088304 |
| hsa-miR-16-5p | MIMAT0000069 | MIRT031690 | Proteomics | Functional MTI (Weak) | 18668040 |
| hsa-miR-1301-3p | MIMAT0005797 | MIRT036001 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-615-3p | MIMAT0003283 | MIRT039936 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-3605-3p | MIMAT0017982 | MIRT052848 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
No target information from mirRecord
- mirRecord
6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 27 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 27126529 | Senescent cells were positive for platelet-derived growth factor receptor-alpha, vimentin, and alpha-smooth muscle actin, specifying myofibroblasts as the predominant cell population undergoing premature senescence in the heart |
| 26603055 | Using laser-assisted microdissection, we found that in rectal cancer samples from patients treated with neoadjuvant CRT, tumor cell niches enriched for senescent cells bookmark regions of increased mRNA expression levels of EMT-related proteins (Slug, Snail, vimentin) compared with the nearby senescent-null tumor cell niches |
| 25941938 | Our group has recently shown that vimentin establishes mitotic polarity in immortalized mammalian cells, and mediates asymmetric partitioning of multiple factors through direct interaction |
| 25915531 | This was accompanied by increased vimentin expression, stress fiber formation, and SFRP1 expression |
| 25472717 | This upregulates the downstream proteins CEBPB, FAK, N-cadherin, vimentin, Oct4 and Sca-1 (also known as stem cell antigen-1), and downregulates E-cadherin |
| 24737666 | Altered vimentin protein expression in human dermal microvascular endothelial cells after ultraviolet or intense pulsed light treatment |
| 24737666 | A recent report suggests that advanced glycosylation end products, especially N() -(carboxymethyl)lysine (CML) modification of vimentin, accelerate the aging process |
| 24737666 | Differential expression and glycation modification of vimentin were found by this approach and further examined by fluorescence-activated cell sorting |
| 24737666 | Among them, vimentin was specifically up-regulated in UV-treated HDMECs |
| 24737666 | CONCLUSION: Vimentin and CML should be useful markers for cell senescence, as well as for evaluating the level of aging |
| 24737666 | Also, targeting increased vimentin expression and its advanced glycation end products could present a target for the treatment of skin aging |
| 24122992 | The cells treated with Doxorubicin (0-500 nm) or vehicle control were analyzed for apoptosis, senescence (SA-beta Galactosidase), and expression of CDKN1A (p21), CDKN1B(p27), CDKN2A (p16), E2F1, vimentin and E-cadherin by immuno-histochemistry and/or Western blot |
| 23841748 | Nevertheless, VPA resulted in upregulation of E-CADHERIN and reduction in VIMENTIN, preventing the skewing of hKEpCs towards a more replicative mesenchymal state required for clonogenic expansion and acquisition of stem cell characters, altogether inducing cell senescence at early passages |
| 23383739 | Vimentin and G-actin cytoskeleton was evaluated both cytometrically and microscopically |
| 23383739 | Here we present preliminary evidence, based on microscopic analyses, that suggest a possible role of vimentin in nuclear alterations accompanying polyploidization-depolyploidization events following genotoxic insults |
| 22916271 | The large number of multiple size and charge isoforms with an altered content that were identified in this study in P7 versus P3, namely the cytoskeleton components beta-actin (7 forms) and vimentin (24 forms), also emphasizes the importance of post-transcriptional modification upon long-term cultivation |
| 21677876 | Interestingly, ADT also induced high levels of vimentin expression in prostate cancer cell lines in vitro and in human prostate tumors in vivo |
| 21649759 | Astrocytes demonstrate age-related changes that resemble those of the SASP: (i) increased level of intermediate glial fibrillary acidic protein and vimentin filaments, (ii) increased expression of several cytokines and (iii) increased accumulation of proteotoxic aggregates |
| 20525429 | Proteome profiling showed significantly more senescence-associated vimentin in FCS-cultured hUCMSCs than in hUCS-cultured hUCMSCs |
| 20397042 | Expression of E-cadherin, vimentin, and fibronectin was also affected |
| 19898866 | METHODS: We analyzed selected markers of senescence and cell death, including possible alterations in vimentin and G-actin cytoskeleton in A549 cells after treatment with doxorubicin |
| 19898866 | Light (SA-beta-galactosidase), fluorescent (vimentin and G-actin labeling) and electron microscopic examinations along with flow cytometry methods (TUNEL, Annexin V/PI staining, cell cycle analysis, intracellular level of vimentin) were employed to determine the outcome of the treatment |
| 19898866 | Some differences in the organization and level of cytoskeletal proteins, especially of vimentin, like fluctuations in its level, were observed |
| 19898866 | On the other hand, G-actin seemed to be more stable than vimentin |
| 18192284 | As opposed to overexpression, we show that mutation of Zeb1 in mice causes a mesenchymal-epithelial transition in gene expression characterized by ectopic expression of epithelial genes such as E-cadherin and loss of expression of mesenchymal genes such as vimentin |
| 17016587 | F6 cells maintained the same properties as of MSCs, such as negativity for both CD117 and vimentin |
| 15742196 | Senescence-associated alterations of cytoskeleton: extraordinary production of vimentin that anchors cytoplasmic p53 in senescent human fibroblasts |
| 15742196 | In the cell senescence, skin fibroblasts extraordinarily produced vimentin in contrast to actin and tubulin, which were down-regulated |
| 15742196 | Senescent cells developed a long and dense vimentin network, long and thin actin fibers, and numerous small focal contact sites, which contrasted with young cells with short and thick actin stress fibers and prominently large focal adhesions |
| 15742196 | A GFP-tagged wild type p53 cDNA was expressed by transfection and shown also to be retained in the cytoplasm in senescent cells, suggesting that p53 is structurally modified to be recognized by PAb240 and anchored to vimentin filaments |
| 14580871 | TGF-betas increased also the expression of the mesenchymal marker vimentin, indicating that basal epithelial cells underwent differentiation with lumenal and mesenchymal features |
| 11702190 | Senescence and cytoskeleton: overproduction of vimentin induces senescent-like morphology in human fibroblasts |
| 11702190 | SDS-gel electrophoresis as well as western blotting demonstrated that there occurred a prominent protein band about 57 kDa in the senescent cells as compared with normal young or immortalized cells growing rapidly, and the protein was identified with a cytoskeletal protein, vimentin |
| 11702190 | In fact, senescent fibroblasts contained approximately threefold more vimentin protein, and fourfold more vimentin mRNA than young embryonic fibroblasts |
| 11702190 | In the senescent cells, vimentin cytoskeleton occurred as densely bundled filaments in parallel with the long axis of cell bodies, whereas in young or actively growing cells it showed short and thin vimentin filaments or fur-like irregular networks |
| 11702190 | It was further demonstrated that senescent cell shapes could be induced when a vimentin expression construct was transfected in young fibroblasts |
| 11702190 | These results suggest that senescent fibroblasts overproduce vimentin protein, and the overproduced vimentin filaments bring about the senescent cell morphology |
| 11344338 | The MK/T-1 cells express vimentin, tubulin, lumican, mimecan, decorin and collagen I, but not keratocan |
| 7796463 | To shed light on the relationship between functions of the cytoskeleton and senescence or immortalization, we investigated the alterations in gene expression after immortalization and measured the amounts of mRNAs for talin, vinculin, alpha-actinin, tropomyosin 1 (TM1), vimentin, lamin A and C, and alpha-tubulin by slot blot and Northern blot analyses |
| 7796463 | We found that the mRNAs for vinculin and vimentin were reduced and the mRNA for lamin A was increased in immortalized cells |
| 7796463 | Vinculin, tropomyosins and vimentin showed their altered distributions in immortalized cells |
| 7963113 | RESULTS: In the stenotic valves nearly all interstitial cells expressed vimentin, and approximately 60% of the cells also expressed alpha-actin and desmin |
| 7963113 | In control valves, fibroblasts expressed vimentin but not alpha-actin or desmin |
| 1917778 | The results of immunoblotting showed that the expression of vimentin was much higher than that of GFAP |
| 1692339 | All of the cell lines expressed keratin intermediate filaments and two showed weak co-expression of vimentin |
| 1692339 | A wide range of keratins were expressed by the tumour xenografts; cornified keratins (K1, K10) were only expressed in the absence of K19 and vimentin, and vice versa |
| 4039326 | The senescence-related increase in interfilament association was also supported by the results of co-precipitation between vimentin and an associated protein of 50,000 D |
| 6733148 | In primary cells still growing on the capsule, alpha B2-crystallin is synthesized in a relatively high amount next to the main cytoskeletal constituents actin, tubulin and vimentin |
| 6733148 | When the cells are subcultured, the synthesis of actin and vimentin becomes more pronounced, while tubulin synthesis is no longer detectable after three transfers |
| 6733148 | The relative amount of vimentin decreases, as compared to actin, during aging and elongation of the cells |
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