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Kinase Fusion Gene:VIM_PDK1 |
Kinase Fusion Protein Summary |
 Kinase Fusion gene summary |
| Kinase Fusion partner gene information | Kinase Fusion gene name: VIM_PDK1 | KinaseFusionDB ID: KFG7062 | FusionGDB2.0 ID: KFG7062 | Hgene | Tgene | Gene symbol | VIM | PDK1 | Gene ID | 7431 | 5170 | |
| Gene name | vimentin | 3-phosphoinositide dependent protein kinase 1 | ||||||||||
| Synonyms | - | PDK1|PDPK2|PDPK2P|PRO0461 | ||||||||||
| Cytomap | 10p13 | 16p13.3 | ||||||||||
| Type of gene | protein-coding | protein-coding | ||||||||||
| Description | vimentinepididymis secretory sperm binding protein | 3-phosphoinositide-dependent protein kinase 13-phosphoinositide-dependent protein kinase 2 pseudogenePkB kinase like gene 1Putative 3-phosphoinositide-dependent protein kinase 2 | ||||||||||
| Modification date | 20240407 | 20240403 | ||||||||||
| UniProtAcc | P08670 | Q15118 | ||||||||||
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000224237, ENST00000485947, ENST00000544301, | ENST00000282077, ENST00000392571, ENST00000410055, ENST00000543905, ENST00000544863, | |||||||||
| Context (manual curation of fusion genes in KinaseFusionDB) | PubMed: VIM [Title/Abstract] AND PDK1 [Title/Abstract] AND fusion [Title/Abstract] | |||||||||||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | VIM(17279592)-PDK1(173450074), # samples:1 | |||||||||||
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | PDK1 | GO:0006468 | protein phosphorylation | 14585963 |
| Tgene | PDK1 | GO:0006469 | negative regulation of protein kinase activity | 9373175 |
| Tgene | PDK1 | GO:0018107 | peptidyl-threonine phosphorylation | 9368760 |
| Tgene | PDK1 | GO:0030512 | negative regulation of transforming growth factor beta receptor signaling pathway | 17327236 |
| Tgene | PDK1 | GO:0032148 | activation of protein kinase B activity | 9368760 |
| Tgene | PDK1 | GO:0035556 | intracellular signal transduction | 14749367 |
| Tgene | PDK1 | GO:0051281 | positive regulation of release of sequestered calcium ion into cytosol | 22454520 |
| Kinase Fusion gene breakpoints across VIM (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Kinase Fusion gene breakpoints across PDK1 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Kinase Fusion Gene Sample Information |
| Kinase Fusion gene information. |
| Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Source | Sample | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp |
| ChiTaRS5.0 | BF338465 | VIM | chr10 | 17279592 | PDK1 | chr2 | 173450074 |
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Kinase Fusion ORF Analysis |
| Kinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Seq length (transcript) | Seq length (amino acids) |
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Kinase Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq |
Multiple Sequence Alignment of All Fusion Protein Isoforms |
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Kinase Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:17279592/:173450074) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VIM | PDK1 |
| 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. {ECO:0000250|UniProtKB:P31000}.; FUNCTION: Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. {ECO:0000269|PubMed:21746880}. | FUNCTION: Kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Plays an important role in cellular responses to hypoxia and is important for cell proliferation under hypoxia. Protects cells against apoptosis in response to hypoxia and oxidative stress. {ECO:0000269|PubMed:17683942, ECO:0000269|PubMed:18541534, ECO:0000269|PubMed:22195962, ECO:0000269|PubMed:7499431}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
| - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
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Kinase-Substrate Information of VIM_PDK1 |
| Phosphorylation target of the kinase (phosphosite, 03-17-2024) |
| Kinase | Kinase UniProt Acc | Kinase species | Substrate | Substrate UniProt Acc | Substrate phosphorylated residues | Substrate phosphorylated sites (+/-7AA) | Domain |
| PDK1 | Q15118 | human | PDHA1 | P08559 | S300 | sMsDPGVsyRtREEI | E1_dh |
| PDK1 | Q15118 | human | PDHA1 | P08559 | S293 | TYRyHGHsMsDPGVs | E1_dh |
| PDK1 | Q15118 | human | PDHA2 | P29803 | S298 | sMsDPGVsyRtREEI | E1_dh |
| PDK1 | Q15118 | human | PDHA1 | P08559 | S232 | NRyGMGtsVERAAAs | E1_dh |
| PDK1 | Q15118 | human | PDHA2 | P29803 | S291 | TYRyHGHsMsDPGVs | E1_dh |
| PDK1 | Q15118 | human | PDHA2 | P29803 | S230 | NLYGMGTsTERAAAS | E1_dh |
| Biological Network Integration of This Kinase and Substrates (GeneMANIA website) |
| Enriched GO biological processes of the phosphorylation target genes of the kinase |
| Kinase | GOID | GO term | P.adjust |
| PDK1 | ID | Description | 0.00e+00 |
| PDK1 | GO:0006086 | acetyl-CoA biosynthetic process from pyruvate | 1.08e-05 |
| PDK1 | GO:0006085 | acetyl-CoA biosynthetic process | 1.50e-05 |
| PDK1 | GO:0006084 | acetyl-CoA metabolic process | 2.60e-05 |
| PDK1 | GO:0006099 | tricarboxylic acid cycle | 2.60e-05 |
| PDK1 | GO:0035384 | thioester biosynthetic process | 3.54e-05 |
| PDK1 | GO:0071616 | acyl-CoA biosynthetic process | 3.54e-05 |
| PDK1 | GO:0033866 | nucleoside bisphosphate biosynthetic process | 3.61e-05 |
| PDK1 | GO:0034030 | ribonucleoside bisphosphate biosynthetic process | 3.61e-05 |
| PDK1 | GO:0034033 | purine nucleoside bisphosphate biosynthetic process | 3.61e-05 |
| PDK1 | GO:0006637 | acyl-CoA metabolic process | 8.15e-05 |
| PDK1 | GO:0035383 | thioester metabolic process | 8.15e-05 |
| PDK1 | GO:0006090 | pyruvate metabolic process | 1.02e-04 |
| PDK1 | GO:0033865 | nucleoside bisphosphate metabolic process | 1.02e-04 |
| PDK1 | GO:0033875 | ribonucleoside bisphosphate metabolic process | 1.02e-04 |
| PDK1 | GO:0034032 | purine nucleoside bisphosphate metabolic process | 1.02e-04 |
| PDK1 | GO:0044272 | sulfur compound biosynthetic process | 1.58e-04 |
| PDK1 | GO:0006006 | glucose metabolic process | 2.11e-04 |
| PDK1 | GO:0009060 | aerobic respiration | 2.11e-04 |
| PDK1 | GO:0009152 | purine ribonucleotide biosynthetic process | 2.34e-04 |
| PDK1 | GO:0009260 | ribonucleotide biosynthetic process | 2.46e-04 |
| PDK1 | GO:0019318 | hexose metabolic process | 2.46e-04 |
| PDK1 | GO:0046390 | ribose phosphate biosynthetic process | 2.46e-04 |
| PDK1 | GO:0045333 | cellular respiration | 2.51e-04 |
| PDK1 | GO:0006164 | purine nucleotide biosynthetic process | 2.67e-04 |
| PDK1 | GO:0005996 | monosaccharide metabolic process | 2.67e-04 |
| PDK1 | GO:0072522 | purine-containing compound biosynthetic process | 2.69e-04 |
| PDK1 | GO:0009165 | nucleotide biosynthetic process | 3.09e-04 |
| PDK1 | GO:1901293 | nucleoside phosphate biosynthetic process | 3.09e-04 |
| PDK1 | GO:0006790 | sulfur compound metabolic process | 3.40e-04 |
| PDK1 | GO:0015980 | energy derivation by oxidation of organic compounds | 3.71e-04 |
| PDK1 | GO:0009150 | purine ribonucleotide metabolic process | 4.21e-04 |
| PDK1 | GO:0009259 | ribonucleotide metabolic process | 4.54e-04 |
| PDK1 | GO:0019693 | ribose phosphate metabolic process | 4.59e-04 |
| PDK1 | GO:0006163 | purine nucleotide metabolic process | 6.18e-04 |
| PDK1 | GO:0072521 | purine-containing compound metabolic process | 6.81e-04 |
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Related Drugs to VIM_PDK1 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
| Distribution of the number of studies mentioning VIM-PDK1 and kinase inhibitors the PubMed Abstract (04-01-2024) |
| Fusion gene - drug pair 1 | Fusion gene - drug pair 2 | PMID | Publication date | DOI | Study title |
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Related Diseases to VIM_PDK1 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Related diseases from the literature mentioned this fusion gene and drug. (PubMed, 04-01-2024) |
| MeSH ID | MeSH term |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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Clinical Trials of the Found Drugs/Small Molecules |
| Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024) |
| Clinical Trials from clinicaltrials.gov (06-17-2024) |
| Fusion Gene | Kinase Inhibitor | NCT ID | Study Status | Phases | Disease | # Enrolment | Date |
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