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Título: | Path2enet: generation of human pathway-derived networks in an expression specific context |
Autor: | Droste, Conrad CSIC ORCID; De Las Rivas, Javier CSIC ORCID CVN | Palabras clave: | Expression R package Bioinformatics Gene coexpression Transcriptomics Network analysis Gene networks Protein network Biological pathway |
Fecha de publicación: | 2016 | Editor: | BioMed Central | Citación: | BMC Genomics 17(Supl.18): 731 (2016) | Resumen: | [Background]: Biological pathways are subsets of the complex biomolecular wiring that occur in living cells. They are usually rationalized and depicted in cartoon maps or charts to show them in a friendly visible way. Despite these efforts to present biological pathways, the current progress of bioinformatics indicates that translation of pathways in networks can be a very useful approach to achieve a computer-based view of the complex processes and interactions that occurr in a living system. [Results]: We have developed a bioinformatic tool called Path2enet that provides a translation of biological pathways in protein networks integrating several layers of information about the biomolecular nodes in a multiplex view. Path2enet is an R package that reads the relations and links between proteins stored in a comprehensive database of biological pathways, KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/ ), and integrates them with expression data from various resources and with data on protein-protein physical interactions. Path2enet tool uses the expression data to determine if a given protein in a network (i.e., a node) is active (ON) or inactive (OFF) in a specific cellular context or sample type. In this way, Path2enet reduces the complexity of the networks and reveals the proteins that are active (expressed) under specific conditions. As a proof of concept, this work presents a practical >case of use> generating the pathway-expression-networks corresponding to the NOTCH Signaling Pathway in human B- and T-lymphocytes. This case is produced by the analysis and integration in Path2enet of an experimental dataset of genome-wide expression microarrays produced with these cell types (i.e., B cells and T cells). [Conclusions]: Path2enet is an open source and open access tool that allows the construction of pathway-expression-networks, reading and integrating the information from biological pathways, protein interactions and gene expression cell specific data. The development of this type of tools aims to provide a more integrative and global view of the links and associations that exist between the proteins working in specific cellular systems. | Versión del editor: | https://doi.org//10.1186/s12864-016-3066-7 | URI: | http://hdl.handle.net/10261/168667 | DOI: | 10.1186/s12864-016-3066-7 | Identificadores: | doi: 10.1186/s12864-016-3066-7 e-issn: 1471-2164 |
Aparece en las colecciones: | (IBMCC) Artículos |
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path2contex.pdf | 2,12 MB | Adobe PDF | Visualizar/Abrir |
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