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Untangling statistical and biological models to understand network inference: The need for a genomics network ontology

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Details

Original languageEnglish
Article numberarticle 229
JournalFrontiers in Genetics
Volume5
Issue numberAUG
DOIs
Publication statusPublished - 2014
Publication typeA1 Journal article-refereed

Abstract

In this paper, we shed light on approaches that are currently used to infer networks from gene expression data with respect to their biological meaning. As we will show, the biological interpretation of these networks depends on the chosen theoretical perspective. For this reason, we distinguish a statistical perspective from a mathematical modeling perspective and elaborate their differences and implications. Our results indicate the imperative need for a genomic network ontology in order to avoid increasing confusion about the biological interpretation of inferred networks, which can be even enhanced by approaches that integrate multiple data sets, respectively, data types.

Keywords

  • Computational genomics, Epistemology, Gene regulatory networks, Genomics network ontology, Mathematical modeling, Statistical inference, Systems biology