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Paper   IPM / Biological / 15559
School of Biological Sciences
  Title:   IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis
1.  Minoo Ashtiani
2.  Payman Nickchi
3.  Soheil Jahangiri Tazehkand
4.  Abdollah Saffari
5.  Mehdi Mirzaei
6.  Mohieddin Jafari
  Status:   Published
  Journal: BMC Bioinformatics
  No.:  1
  Vol.:  20
  Year:  2019
  Pages:   73
  Supported by:  IPM
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.

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