title: Improving biomarker list stability by integration of biological knowledge in the learning process.
abstract: BACKGROUND
  The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for biomarker discovery using microarray data often provide results with limited overlap. It has been suggested that one reason for these inconsistencies may be that in complex diseases, such as cancer, multiple genes belonging to one or more physiological pathways are associated with the outcomes. Thus, a possible approach to improve list stability is to integrate biological information from genomic databases in the learning process; however, a comprehensive assessment based on different types of biological information is still lacking in the literature. In this work we have compared the effect of using different biological information in the learning process like functional annotations, protein-protein interactions and expression correlation among genes.
  
  
  RESULTS
  Biological knowledge has been codified by means of gene similarity matrices and expression data linearly transformed in such a way that the more similar two features are, the more closely they are mapped. Two semantic similarity matrices, based on Biological Process and Molecular Function Gene Ontology annotation, and geodesic distance applied on protein-protein interaction networks, are the best performers in improving list stability maintaining almost equal prediction accuracy.
  
  
  CONCLUSIONS
  The performed analysis supports the idea that when some features are strongly correlated to each other, for example because are close in the protein-protein interaction network, then they might have similar importance and are equally relevant for the task at hand. Obtained results can be a starting point for additional experiments on combining similarity matrices in order to obtain even more stable lists of biomarkers. The implementation of the classification algorithm is available at the link: http://www.math.unipd.it/~dasan/biomarkers.html.
authors.affiliation: Department of Information Engineering, University of Padova, via G, Gradenigo 6/B, 35131 Padova, Italy.
authors.forename: Tiziana
authors.initials: T
authors.lastname: Sanavia
authors.forename: Fabio
authors.initials: F
authors.lastname: Aiolli
authors.forename: Giovanni
authors.initials: G
authors.lastname: Da San Martino
authors.forename: Andrea
authors.initials: A
authors.lastname: Bisognin
authors.forename: Barbara
authors.initials: B
authors.lastname: Di Camillo
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D015415:Biomarkers / Q000032:analysis; D001943:Breast Neoplasms / Q000235:genetics*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D060066:Protein Interaction Maps; D018875:Vocabulary, Controlled
chemical_list: D015415:Biomarkers