MTGO: PPI Network Analysis Via Topological and Functional Module Identification

Danila Vella, Simone Marini, Francesca Vitali, Dario Di Silvestre, Giancarlo Mauri, Riccardo Bellazzi

Research output: Contribution to journalArticle

Abstract

Protein-protein interaction (PPI) networks are viable tools to understand cell functions, disease machinery, and drug design/repositioning. Interpreting a PPI, however, it is a particularly challenging task because of network complexity. Several algorithms have been proposed for an automatic PPI interpretation, at first by solely considering the network topology, and later by integrating Gene Ontology (GO) terms as node similarity attributes. Here we present MTGO - Module detection via Topological information and GO knowledge, a novel functional module identification approach. MTGO let emerge the bimolecular machinery underpinning PPI networks by leveraging on both biological knowledge and topological properties. In particular, it directly exploits GO terms during the module assembling process, and labels each module with its best fit GO term, easing its functional interpretation. MTGO shows largely better results than other state of the art algorithms (including recent GO-based ones) when searching for small or sparse functional modules, while providing comparable or better results all other cases. MTGO correctly identifies molecular complexes and literature-consistent processes in an experimentally derived PPI network of Myocardial infarction. A software version of MTGO is available freely for non-commercial purposes at https://gitlab.com/d1vella/MTGO .

Original languageEnglish
Pages (from-to)5499
JournalScientific Reports
Volume8
Issue number1
DOIs
Publication statusPublished - Apr 3 2018

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Protein Interaction Maps
Gene Ontology
Proteins
Drug Repositioning
Drug Design
Software
Myocardial Infarction

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MTGO : PPI Network Analysis Via Topological and Functional Module Identification. / Vella, Danila; Marini, Simone; Vitali, Francesca; Di Silvestre, Dario; Mauri, Giancarlo; Bellazzi, Riccardo.

In: Scientific Reports, Vol. 8, No. 1, 03.04.2018, p. 5499.

Research output: Contribution to journalArticle

Vella, Danila ; Marini, Simone ; Vitali, Francesca ; Di Silvestre, Dario ; Mauri, Giancarlo ; Bellazzi, Riccardo. / MTGO : PPI Network Analysis Via Topological and Functional Module Identification. In: Scientific Reports. 2018 ; Vol. 8, No. 1. pp. 5499.
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