PANEV: an R package for a pathway-based network visualization
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s12859-020-3371-7 http://hdl.handle.net/11449/196569 |
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. |
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PANEV: an R package for a pathway-based network visualizationMolecular pathwaysPathway visualizationGenomic and transcriptomic analysisData miningKEGGBackground 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.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Univ Molise, Dipartimento Agr Ambiente & Alimenti, I-86100 Campobasso, ItalySao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, BR-16050680 Aracatuba, SP, BrazilUniv Cattolica Sacro Cuore, Ist Zootecn, I-29122 Piacenza, ItalyUniv Molise, Dipartimento Biosci & Territorio, I-86090 Pesche, IS, ItalyUniv Perugia, Dipartimento Med Vet, I-06126 Perugia, ItalyUniv Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, ItalySao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, BR-16050680 Aracatuba, SP, BrazilFAPESP: 2016/05787-7BmcUniv MoliseUniversidade Estadual Paulista (Unesp)Univ Cattolica Sacro CuoreUniv PerugiaUniv UdinePalombo, ValentinoMilanesi, Marco [UNESP]Sferra, GabriellaCapomaccio, StefanoSgorlon, SandyD'Andrea, Mariasilvia2020-12-10T19:49:10Z2020-12-10T19:49:10Z2020-02-06info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article7http://dx.doi.org/10.1186/s12859-020-3371-7Bmc Bioinformatics. London: Bmc, v. 21, n. 1, 7 p., 2020.1471-2105http://hdl.handle.net/11449/19656910.1186/s12859-020-3371-7WOS:000512751600001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBmc Bioinformaticsinfo:eu-repo/semantics/openAccess2024-09-04T19:16:19Zoai:repositorio.unesp.br:11449/196569Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestrepositoriounesp@unesp.bropendoar:29462024-09-04T19:16:19Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
PANEV: an R package for a pathway-based network visualization |
title |
PANEV: an R package for a pathway-based network visualization |
spellingShingle |
PANEV: an R package for a pathway-based network visualization Palombo, Valentino Molecular pathways Pathway visualization Genomic and transcriptomic analysis Data mining KEGG |
title_short |
PANEV: an R package for a pathway-based network visualization |
title_full |
PANEV: an R package for a pathway-based network visualization |
title_fullStr |
PANEV: an R package for a pathway-based network visualization |
title_full_unstemmed |
PANEV: an R package for a pathway-based network visualization |
title_sort |
PANEV: an R package for a pathway-based network visualization |
author |
Palombo, Valentino |
author_facet |
Palombo, Valentino Milanesi, Marco [UNESP] Sferra, Gabriella Capomaccio, Stefano Sgorlon, Sandy D'Andrea, Mariasilvia |
author_role |
author |
author2 |
Milanesi, Marco [UNESP] Sferra, Gabriella Capomaccio, Stefano Sgorlon, Sandy D'Andrea, Mariasilvia |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Univ Molise Universidade Estadual Paulista (Unesp) Univ Cattolica Sacro Cuore Univ Perugia Univ Udine |
dc.contributor.author.fl_str_mv |
Palombo, Valentino Milanesi, Marco [UNESP] Sferra, Gabriella Capomaccio, Stefano Sgorlon, Sandy D'Andrea, Mariasilvia |
dc.subject.por.fl_str_mv |
Molecular pathways Pathway visualization Genomic and transcriptomic analysis Data mining KEGG |
topic |
Molecular pathways Pathway visualization Genomic and transcriptomic analysis Data mining KEGG |
description |
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. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-10T19:49:10Z 2020-12-10T19:49:10Z 2020-02-06 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1186/s12859-020-3371-7 Bmc Bioinformatics. London: Bmc, v. 21, n. 1, 7 p., 2020. 1471-2105 http://hdl.handle.net/11449/196569 10.1186/s12859-020-3371-7 WOS:000512751600001 |
url |
http://dx.doi.org/10.1186/s12859-020-3371-7 http://hdl.handle.net/11449/196569 |
identifier_str_mv |
Bmc Bioinformatics. London: Bmc, v. 21, n. 1, 7 p., 2020. 1471-2105 10.1186/s12859-020-3371-7 WOS:000512751600001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Bmc Bioinformatics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
7 |
dc.publisher.none.fl_str_mv |
Bmc |
publisher.none.fl_str_mv |
Bmc |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
repositoriounesp@unesp.br |
_version_ |
1810021423734849536 |