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.

Vella, D., Marini, S., Vitali, F., Di Silvestre, D., Mauri, G., Bellazzi, R. (2018). MTGO: PPI Network Analysis Via Topological and Functional Module Identification. SCIENTIFIC REPORTS, 8(1) [10.1038/s41598-018-23672-0].

MTGO: PPI Network Analysis Via Topological and Functional Module Identification

Vella, D;Mauri, G;
2018

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.
Articolo in rivista - Articolo scientifico
Clustering algorithm, Gene Ontology, biological network
English
2018
8
1
5499
open
Vella, D., Marini, S., Vitali, F., Di Silvestre, D., Mauri, G., Bellazzi, R. (2018). MTGO: PPI Network Analysis Via Topological and Functional Module Identification. SCIENTIFIC REPORTS, 8(1) [10.1038/s41598-018-23672-0].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/195368
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