IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis.

TitleIMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis.
Publication TypeJournal Article
Year of Publication2019
AuthorsAshtiani M, Nickchi P, Jahangiri-Tazehkand S, Safari A, Mirzaie M, Jafari M
JournalBMC Bioinformatics
Volume20
Issue1
Pagination73
Date Published02/2019
ISSN1471-2105
Abstract

BACKGROUND: Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Also, lack of a standard PPIN limits us in the comparison studies and results in the incompatible outcomes. Using an evolution-based concept, i.e. interolog which refers to interacting orthologous protein sets, pave the way toward an optimal benchmark.

RESULTS: Here, we provide an R package, IMMAN, as a tool for reconstructing Interolog Protein Network (IPN) by integrating several Protein-protein Interaction Networks (PPINs). Users can unify different PPINs to mine conserved common networks among species. IMMAN is designed to retrieve IPNs with different degrees of conservation to engage prediction analysis of protein functions according to their networks.

CONCLUSIONS: IPN consists of evolutionarily conserved nodes and their related edges regarding low false positive rates, which can be considered as a gold standard network in the contexts of biological network analysis regarding to those PPINs which is derived from.

DOI10.1186/s12859-019-2659-y
Alternate JournalBMC Bioinformatics
PubMed ID30755155
PubMed Central IDPMC6373071