Learning the local Bayesian network structure around the ZNF217 oncogene in breast tumours

Authors:
Emmanuel Prestat;SéRgio Rodrigues De Morais;Julie A. Vendrell;AuréLie Thollet;Christian Gautier;Pascale A Cohen;Alex Aussem
Affiliations:
Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France and CNRS, UMR5558, Laboratoire de Biométrie et Biologie ívolutive, Université Lyon 1, 696 ...;Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France;Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France and Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France and CNRS UMR5286, ...;Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France and Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France and CNRS UMR5286, ...;Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France and CNRS, UMR5558, Laboratoire de Biométrie et Biologie ívolutive, Université Lyon 1, 696 ...;Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France and Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France and CNRS UMR5286, ...;Université de Lyon, 69000, Lyon, France and Université Lyon 1, 69000 Lyon, France and CNRS, UMR5205, Laboratoire d'Informatique en Image et Systèmes d'information, 69622 Villeurbann ...
Venue:
Computers in Biology and Medicine
Year:
2013

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Abstract

In this study, we discuss and apply a novel and efficient algorithm for learning a local Bayesian network model in the vicinity of the ZNF217 oncogene from breast cancer microarray data without having to decide in advance which genes have to be included in the learning process. ZNF217 is a candidate oncogene located at 20q13, a chromosomal region frequently amplified in breast and ovarian cancer, and correlated with shorter patient survival in these cancers. To properly address the difficulties in managing complex gene interactions given our limited sample, statistical significance of edge strengths was evaluated using bootstrapping and the less reliable edges were pruned to increase the network robustness. We found that 13 out of the 35 genes associated with deregulated ZNF217 expression in breast tumours have been previously associated with survival and/or prognosis in cancers. Identifying genes involved in lipid metabolism opens new fields of investigation to decipher the molecular mechanisms driven by the ZNF217 oncogene. Moreover, nine of the 13 genes have already been identified as putative ZNF217 targets by independent biological studies. We therefore suggest that the algorithms for inferring local BNs are valuable data mining tools for unraveling complex mechanisms of biological pathways from expression data. The source code is available at http://www710.univ-lyon1.fr/~aaussem/Software.html.