molecular network Dotaz Zobrazit nápovědu
elektronický časopis
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- biologie
- biochemie
- genetika, lékařská genetika
- NLK Publikační typ
- elektronické časopisy
- MeSH
- antifungální látky metabolismus MeSH
- finanční podpora výzkumu jako téma MeSH
- fungicidy průmyslové metabolismus MeSH
- geny hub fyziologie MeSH
- kvasinky fyziologie účinky léků MeSH
- membránové proteiny fyziologie MeSH
- mnohočetná léková rezistence genetika MeSH
- transkripční faktory fyziologie MeSH
- Publikační typ
- přehledy MeSH
- MeSH
- aktiny MeSH
- dendrity fyziologie chemie ultrastruktura MeSH
- lidé MeSH
- molekulární konformace MeSH
- mozková kůra fyziologie ultrastruktura MeSH
- neuroplasticita MeSH
- neurotransmiterové látky fyziologie MeSH
- synapse fyziologie chemie ultrastruktura MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- přehledy MeSH
Current innovations in molecular biology series ; Vol. 3
[1st ed.] 187 s.
- Konspekt
- Lékařské vědy. Lékařství
- NLK Obory
- lékařská informatika
- biologie
SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.
- MeSH
- software * MeSH
- systémová biologie * MeSH
- Publikační typ
- časopisecké články MeSH
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
- MeSH
- hmotnostní spektrometrie metody MeSH
- internet MeSH
- ionty chemie metabolismus MeSH
- metabolické sítě a dráhy * MeSH
- metabolomika metody MeSH
- molekulární struktura MeSH
- reprodukovatelnost výsledků MeSH
- software MeSH
- výpočetní biologie metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
elektronický časopis
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- onkologie
- genetika, lékařská genetika
- NLK Publikační typ
- elektronické časopisy
INTRODUCTION: This study aimed to identify the phytochemical constituents that could target gastric cancer in Kangai injection using a network pharmacology-based approach. METHODS: Protein-protein interactions (PPI), Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted utilizing String and OmicShare tools. In the in vitro experiments, the related mRNA and protein levels were assessed via real-time quantitative polymerase chain reaction and Western blotting, respectively. Cell proliferation was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay. RESULTS: Kangai injection comprises several compounds, which target multiple substrates and pathways related to gastric cancer. The PPI and Gene Ontology analyses revealed that tumor necrosis factor (TNF) was a hub gene. KEGG pathway enrichment analysis indicated that the the TNF pathway was significantly enriched. Kangai injection decreased the mRNA levels of TNFR2, TRAF2, PI3K, AKT, and IκBα and inhibited the phosphorylation of PI3K, AKT, and IκBα phosphorylations. Kangai injection inhibited cell proliferation, while TNFR2 overexpression or treatment with the PI3K activator 740 Y-P partially restored it. CONCLUSION: Kangai injection operates through multiple targets and pathways in gastric cancer, with the TNFR2/PI3K/AKT/NF-κB pathway playing a crucial role in its mechanism against gastric cancer.
- MeSH
- fosfatidylinositol-3-kinasy MeSH
- lidé MeSH
- nádory žaludku * farmakoterapie genetika MeSH
- NFKB inhibitor alfa MeSH
- protoonkogenní proteiny c-akt MeSH
- receptory TNF - typ II MeSH
- síťová farmakologie MeSH
- TNF-alfa genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
