PANEV: an R package for a pathway-based network visualization
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Data
2020-02-06
Autores
Palombo, Valentino
Milanesi, Marco [UNESP]
Sferra, Gabriella
Capomaccio, Stefano
Sgorlon, Sandy
D'Andrea, Mariasilvia
Título da Revista
ISSN da Revista
Título de Volume
Editor
Bmc
Resumo
Background During the last decade, with the aim to solve the challenge of post-genomic and transcriptomic data mining, a plethora of tools have been developed to create, edit and analyze metabolic pathways. In particular, when a complex phenomenon is considered, the creation of a network of multiple interconnected pathways of interest could be useful to investigate the underlying biology and ultimately identify functional candidate genes affecting the trait under investigation. Results PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes. Conclusions The suite has no species constraints and it is ready to analyze genomic or transcriptomic outcomes. Users need to supply the list of candidate genes, specify the target pathway(s) and the number of interconnected downstream and upstream pathways (levels) required for the investigation. The package is available at https://github.com/vpalombo/PANEV.
Descrição
Palavras-chave
Molecular pathways, Pathway visualization, Genomic and transcriptomic analysis, Data mining, KEGG
Como citar
Bmc Bioinformatics. London: Bmc, v. 21, n. 1, 7 p., 2020.