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Constructing Probabilistic Genetic Networks of Plasmodium falciparum from Dynamical Expression Signals of the Intraerythrocytic Development Cycle

  • Junior Barrera
  • Roberto M. CesarJr.
  • David C. MartinsJr.
  • Ricardo Z. N. Vêncio
  • Emilio F. Merino
  • Márcio M. Yamamoto
  • Florencia G. Leonardi
  • Carlos A. de B. Pereira
  • Hernando A. del Portillo

Abstract

The completion of the genome sequence of Plasmodium falciparum revealed that close to 60% of the annotated genome corresponds to hypothetical proteins and that many genes, whose metabolic pathways or biological products are known, have not been predicted from sequence similarity searches. Recently, using global gene expression of the asexual blood stages of P. falciparum at 1 h resolution scale and Discrete Fourier Transform based techniques, it has been demonstrated that many genes are regulated in a single periodic manner during the asexual blood stages. Moreover, by ordering the genes according to the phase of expression, a new list of targets for vaccine and drug development was generated. In the present paper, genes are annotated under a different perspective: a list of functional properties is attributed to networks of genes representing subsystems of the P. falciparum regulatory expression system. The model developed to represent genetic networks, called Probabilistic Genetic Network (PGN), is a Markov chain with some additional properties. This model mimics the properties of a gene as a non-linear stochastic gate and the systems are built by coupling of these gates. Moreover, a tool that integrates mining of dynamical expression signals by PGN design techniques, different databases and biological knowledge, was developed. The applicability of this tool for discovering gene networks of the malaria expression regulation system has been validated using the glycolytic pathway as a “gold-standard”, as well as by creating an apicoplast PGN network. Presently, we are tentatively improving the network design technique before trying to validate results from the apicoplast PGN network through reverse genetics approaches.

Keywords

malaria annotation tool probabilistic genetic networks dynamical system Markov chain mutual information gene expression microarrays 

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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Junior Barrera
    • 1
  • Roberto M. CesarJr.
    • 1
  • David C. MartinsJr.
    • 1
  • Ricardo Z. N. Vêncio
    • 1
  • Emilio F. Merino
    • 2
  • Márcio M. Yamamoto
    • 2
  • Florencia G. Leonardi
    • 1
  • Carlos A. de B. Pereira
    • 1
  • Hernando A. del Portillo
    • 2
  1. 1.Instituto de Matemáticas e Estatística e BIOINFO-USP, Núcleo de Pesquisas em BioinformáticaUniversidade de São PauloSão Paulo, SPBrazil
  2. 2.Instituto De Ciências Biomédicas, Departamento de ParasitologiaUniversidade de São PauloSão Paulo, SPBrazil

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