PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes.

ABSTRACT: Identification of microbial functional association networks allows interpretation of biological phenomena and a greater understanding of the molecular basis of pathogenicity and also underpins the formulation of control measures. Here, we describe PPNet, a tool that uses genome information and analysis of phylogenetic profiles with binary similarity and distance measures to derive large-scale bacterial gene association networks of a single species. As an exemplar, we have derived a functional association network in the pig pathogen Streptococcus suis using 81 binary similarity and dissimilarity measures which demonstrates excellent performance based on the area under the receiver operating characteristic (AUROC), the area under the precision-recall (AUPR), and a derived overall scoring met

SUBMITTER: Li Y 

PROVIDER: S-EPMC9927313 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature