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EURASIP Journal on Bioinformatics and Systems Biology

, 2015:10

First Online: 11 November 2015Received: 12 August 2015Accepted: 30 October 2015


Biological networks inherently have uncertain topologies. This arises from many factors. For instance, interactions between molecules may or may not take place under varying conditions. Genetic or epigenetic mutations may also alter biological processes like transcription or translation. This uncertainty is often modeled by associating each interaction with a probability value. Studying biological networks under this probabilistic model has already been shown to yield accurate and insightful analysis of interaction data. However, the problem of assigning accurate probability values to interactions remains unresolved. In this paper, we present a novel method for computing interaction probabilities in signaling networks based on transcription levels of genes. The transcription levels define the signal reachability probability between membrane receptors and transcription factors. Our method computes the interaction probabilities that minimize the gap between the observed and the computed signal reachability probabilities. We evaluate our method on four signaling networks from the Kyoto Encyclopedia of Genes and Genomes KEGG. For each network, we compute its edge probabilities using the gene expression profiles for seven major leukemia subtypes. We use these values to analyze how the stress induced by different leukemia subtypes affects signaling interactions.

KeywordsBiological networks Signaling Interaction probability Reachability Leukemia  Download fulltext PDF

Autor: Haitham Gabr - Juan Carlos Rivera-Mulia - David M. Gilbert - Tamer Kahveci


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