Gene regulatory network expansion is a task of the foremost importance in computational biology that aims at finding new genes to expand a given known gene regulatory network. To this end we present OneGenE, a novel framework for gene regulatory network expansion that relies on the BOINC platform. OneGenE is an evolution of the NES2RA algorithm, with the aim to overcome its main criticality, i.e. long response time for the final user. To achieve this goal, candidate expansion lists are pre-computed for each gene in the organism and then aggregated at runtime to produce the the final expansion list for a given known gene regulatory network. We validated OneGenE on the expression data of Pseudomonas aeruginosa, comparing its results with the one obtained by NES2RA and through a biological literature review.

OneGenE: Regulatory Gene Network Expansion via Distributed Volunteer Computing on BOINC / Asnicar, Francesco; Masera, Luca; Pistore, Davide; Valentini, Samuel; Cavecchia, Valter; Blanzieri, Enrico. - (2019), pp. 315-322. ((Intervento presentato al convegno PDP 2019 tenutosi a Pavia nel 13th-15th February 2019 [10.1109/EMPDP.2019.8671629].

OneGenE: Regulatory Gene Network Expansion via Distributed Volunteer Computing on BOINC

Asnicar, Francesco;Masera, Luca;Valentini, Samuel;Cavecchia, Valter;Blanzieri, Enrico
2019

Abstract

Gene regulatory network expansion is a task of the foremost importance in computational biology that aims at finding new genes to expand a given known gene regulatory network. To this end we present OneGenE, a novel framework for gene regulatory network expansion that relies on the BOINC platform. OneGenE is an evolution of the NES2RA algorithm, with the aim to overcome its main criticality, i.e. long response time for the final user. To achieve this goal, candidate expansion lists are pre-computed for each gene in the organism and then aggregated at runtime to produce the the final expansion list for a given known gene regulatory network. We validated OneGenE on the expression data of Pseudomonas aeruginosa, comparing its results with the one obtained by NES2RA and through a biological literature review.
Proceedings 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, PDP 2019
Piscataway, NJ
Institute of Electrical and Electronics Engineers Inc.
9781728116440
Asnicar, Francesco; Masera, Luca; Pistore, Davide; Valentini, Samuel; Cavecchia, Valter; Blanzieri, Enrico
OneGenE: Regulatory Gene Network Expansion via Distributed Volunteer Computing on BOINC / Asnicar, Francesco; Masera, Luca; Pistore, Davide; Valentini, Samuel; Cavecchia, Valter; Blanzieri, Enrico. - (2019), pp. 315-322. ((Intervento presentato al convegno PDP 2019 tenutosi a Pavia nel 13th-15th February 2019 [10.1109/EMPDP.2019.8671629].
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11572/235624
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