title: Pathway analysis of high-throughput biological data within a Bayesian network framework.
abstract: BACKGROUND
  Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network.
  
  
  RESULTS
  Proposed method takes into account the connectivity and relatedness between nodes of the pathway through factoring pathway topology in its model. Our simulations using synthetic data demonstrated robustness of our approach. We tested proposed method, Bayesian Pathway Analysis (BPA), on human microarray data regarding renal cell carcinoma (RCC) and compared our results with gene set enrichment analysis. BPA was able to find broader and more specific pathways related to RCC.
  
  
  BACKGROUND
  Accompanying BPA software (BPAS) package is freely available for academic use at http://bumil.boun.edu.tr/bpa.
authors.affiliation: Bogazici University, Institute of Biomedical Engineering, 34342, Istanbul, Turkey.
authors.forename: Senol
authors.initials: S
authors.lastname: Isci
authors.forename: Cengizhan
authors.initials: C
authors.lastname: Ozturk
authors.forename: Jon
authors.initials: J
authors.lastname: Jones
authors.forename: Hasan H
authors.initials: HH
authors.lastname: Otu
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D002292:Carcinoma, Renal Cell / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D057166:High-Throughput Screening Assays; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D012984:Software