title: Integration of Pathway Knowledge and Dynamic Bayesian Networks for the Prediction of Oral Cancer Recurrence.
abstract: Oral squamous cell carcinoma has been characterized as a complex disease which involves dynamic genomic changes at the molecular level. These changes indicate the worth to explore the interactions of the molecules and especially of differentially expressed genes that contribute to cancer progression. Moreover, based on this knowledge the identification of differentially expressed genes and related molecular pathways is of great importance. In the present study, we exploit differentially expressed genes in order to further perform pathway enrichment analysis. According to our results we found significant pathways in which the disease associated genes have been identified as strongly enriched. Furthermore, based on the results of the pathway enrichment analysis we propose a methodology for predicting oral cancer recurrence using dynamic Bayesian networks. The methodology takes into consideration time series gene expression data in order to predict a disease recurrence. Subsequently, we are able to conjecture about the causal interactions between genes in consecutive time intervals. Concerning the performance of the predictive models, the overall accuracy of the algorithm is 81.8% and the area under the ROC curve 89.2% regarding the knowledge from the overrepresented pre-NOTCH Expression and processing pathway.
authors.forename: Konstantina
authors.initials: K
authors.lastname: Kourou
authors.forename: Costas
authors.initials: C
authors.lastname: Papaloukas
authors.forename: Dimitrios I
authors.initials: DI
authors.lastname: Fotiadis
mesh_terms: D000465:Algorithms; D002294:Carcinoma, Squamous Cell / Q000453:epidemiology / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D015233:Models, Statistical; D009062:Mouth Neoplasms / Q000453:epidemiology / Q000235:genetics* / Q000378:metabolism; D009364:Neoplasm Recurrence, Local / Q000453:epidemiology / Q000235:genetics* / Q000378:metabolism; D012372:ROC Curve; D015398:Signal Transduction / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics