A Boolean approach to linear prediction for signaling network modeling

F. Eduati, A. Corradin, B. Di Camillo, G. Toffolo

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)

Abstract

The task of the DREAM4 (Dialogue for Reverse Engineering Assessments and Methods) "Predictive signaling network modeling" challenge was to develop a method that, from single-stimulus/inhibitor data, reconstructs a cause-effect network to be used to predict the protein activity level in multi-stimulus/inhibitor experimental conditions. The method presented in this paper, one of the best performing in this challenge, consists of 3 steps: 1. Boolean tables are inferred from single-stimulus/inhibitor data to classify whether a particular combination of stimulus and inhibitor is affecting the protein. 2. A cause-effect network is reconstructed starting from these tables. 3. Training data are linearly combined according to rules inferred from the reconstructed network. This method, although simple, permits one to achieve a good performance providing reasonable predictions based on a reconstructed network compatible with knowledge from the literature. It can be potentially used to predict how signaling pathways are affected by different ligands and how this response is altered by diseases.

Original languageEnglish
JournalPLoS ONE
Volume5
Issue number9
DOIs
Publication statusPublished - 16 Sep 2010
Externally publishedYes

Keywords

  • Algorithms
  • Computational Biology
  • Gene Regulatory Networks
  • Humans
  • Linear Models
  • Models, Biological
  • Proteins
  • Signal Transduction
  • Evaluation Studies
  • Journal Article
  • Research Support, Non-U.S. Gov't

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