Molecular interplay between organisms by phylogenetic profiling

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1 Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanità, Roma, Italia
2 Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Pesche, Isernia, Italia
DOI
10.7287/peerj.preprints.27373v1
Published
Accepted
Subject Areas
Bioinformatics, Parasitology, Infectious Diseases, Computational Science
Keywords
systems biology, bioinformatics, parasitology, malaria, protein-protein interactions, host-pathogen interactions, infectious diseases
Copyright
© 2018 Sferra et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Sferra G, Ponzi M, Pizzi E. 2018. Molecular interplay between organisms by phylogenetic profiling. PeerJ Preprints 6:e27373v1

Abstract

In recent years, several computational methods have been developed to predict protein-protein interactions (PPIs) at a genome-wide level. Between them phylogenetic profiling is routinely used to infer PPIs occurring within an organism. Recent improvements of the methods rely on the usage of large genomic datasets and on the distance correlation, a correlation-based measure, as novel measure of profile similarity. Here we adapted the robust improved phylogenetic profiling strategy to predict PPIs occurring between organisms. Specifically, we inferred PPIs occurring in the host-parasite system of Plasmodium falciparum, the deadliest human malaria parasite, and the human erythrocyte, in which the parasite performs an asexual reproduction and that is responsible of the greatest part of the parasitosis symptoms. By applying the method we could predict host-host, erythrocyte-erythrocyte and host-erythrocyte PPIs. As proof of principle, we demonstrated that the phylogenetic profiling can be extended to predict interactions that not necessarily are performed by proteins belonging to the same organism.

Author Comment

“This is an abstract which has been accepted for the BBCC2018 Conference