| Full text | |
| Author(s): |
Palombo, Valentino
[1]
;
Milanesi, Marco
[2, 3]
;
Sferra, Gabriella
[4]
;
Capomaccio, Stefano
[2, 5]
;
Sgorlon, Sandy
[6]
;
D'Andrea, Mariasilvia
[1]
Total Authors: 6
|
| Affiliation: | [1] Univ Molise, Dipartimento Agr Ambiente & Alimenti, I-86100 Campobasso - Italy
[2] Univ Cattolica Sacro Cuore, Ist Zootecn, I-29122 Piacenza - Italy
[3] Sao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, BR-16050680 Aracatuba, SP - Brazil
[4] Univ Molise, Dipartimento Biosci & Territorio, I-86090 Pesche, IS - Italy
[5] Univ Perugia, Dipartimento Med Vet, I-06126 Perugia - Italy
[6] Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine - Italy
Total Affiliations: 6
|
| Document type: | Journal article |
| Source: | BMC Bioinformatics; v. 21, n. 1 FEB 6 2020. |
| Web of Science Citations: | 0 |
| Abstract | |
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. (AU) | |
| FAPESP's process: | 16/05787-7 - Combining high-density SNP genotypes and next generation sequence data to map disadvantageous genetic variants in Nellore cattle |
| Grantee: | Marco Milanesi |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |