BMC Bioinformatics
| العنوان: | BMC Bioinformatics |
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| المؤلفون: | Anna Ritz, Ibrahim Youssef, Jeffrey N. Law |
| المصدر: | BMC Bioinformatics BMC Bioinformatics, Vol 20, Iss S16, Pp 1-15 (2019) BIBM |
| بيانات النشر: | BioMed Central, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 0301 basic medicine, Cell signaling, Signaling pathways, Computer science, Systems biology, Computational biology, lcsh:Computer applications to medicine. Medical informatics, Interactome, Biochemistry, Protein–protein interaction, 03 medical and health sciences, Automation, 0302 clinical medicine, Protein-protein interaction, Structural Biology, Protein Interaction Mapping, Humans, Molecular Biology, lcsh:QH301-705.5, Cellular compartment, 030304 developmental biology, 0303 health sciences, Applied Mathematics, Research, Biological networks, Protein localization, Computational Biology, Proteins, Protein subcellular localization prediction, Computer Science Applications, Protein Transport, 030104 developmental biology, Membrane, lcsh:Biology (General), 030220 oncology & carcinogenesis, lcsh:R858-859.7, DNA microarray, Signal transduction, 030217 neurology & neurosurgery, Biological network, Algorithms, Protein Binding, Signal Transduction |
| الوصف: | Background Understanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists generate testable hypotheses about signaling. However, automatic reconstruction of signaling pathways suffers from many interactions with the same confidence score leading to many equally good candidates. Further, some reconstructions are biologically misleading due to ignoring protein localization information. Results We propose LocPL, a method to improve the automatic reconstruction of signaling pathways from PPIs by incorporating information about protein localization in the reconstructions. The method relies on a dynamic program to ensure that the proteins in a reconstruction are localized in cellular compartments that are consistent with signal transduction from the membrane to the nucleus. LocPL and existing reconstruction algorithms are applied to two PPI networks and assessed using both global and local definitions of accuracy. LocPL produces more accurate and biologically meaningful reconstructions on a versatile set of signaling pathways. Conclusion LocPL is a powerful tool to automatically reconstruct signaling pathways from PPIs that leverages cellular localization information about proteins. The underlying dynamic program and signaling model are flexible enough to study cellular signaling under different settings of signaling flow across the cellular compartments. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1471-2105 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::501ab81b4fbb9a2fbde6f73bc38548e4 http://europepmc.org/articles/PMC6886211 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....501ab81b4fbb9a2fbde6f73bc38548e4 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 14712105 |
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