Asymmetric Comparison and Querying of Biological Networks

Simona Ester Rombo, Simona E. Rombo, Nicola Ferraro, Simona Panni, Luigi Palopoli

Risultato della ricerca: Article

17 Citazioni (Scopus)

Abstract

Comparing and querying the protein-protein interaction (PPI) networks of different organisms is important to inferknowledge about conservation across species. Known methods that perform these tasks operate symmetrically, i.e., they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how the corresponding organism is biologically well characterized. In this paper a new idea is developed, that is, to exploit differences in the characterization of organisms at hand in order to devise methods for comparing their PPI networks. We use the PPI network (called Master) of the best characterized organism as a fingerprint to guide the alignment process to the second input network (called Slave), so that generated results preferably retain the structural characteristics of the Master network. Technically, this is obtained by generating from the Master a finite automaton, called alignment model, which is then fed with (a linearization of) the Slave for thepurpose of extracting, via the Viterbi algorithm, matching subgraphs. We propose an approach able to perform global alignment and network querying, and we apply it on PPI networks. We tested our method showing that the results it returns are biologically relevant.
Lingua originaleEnglish
pagine (da-a)876-889
Numero di pagine13
RivistaIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume8
Stato di pubblicazionePublished - 2011

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics
  • Applied Mathematics

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