title: Learning the structure of gene regulatory networks from time series gene expression data.
abstract: BACKGROUND
  Dynamic Bayesian Network (DBN) is an approach widely used for reconstruction of gene regulatory networks from time-series microarray data. Its performance in network reconstruction depends on a structure learning algorithm. REVEAL (REVerse Engineering ALgorithm) is one of the algorithms implemented for learning DBN structure and used to reconstruct gene regulatory networks (GRN). However, the two-stage temporal Bayes network (2TBN) structure of DBN that specifies correlation between time slices cannot be obtained by score metrics used in REVEAL.
  
  
  METHODS
  In this paper, we study a more sophisticated score function for DBN first proposed by Nir Friedman for stationary DBNs structure learning of both initial and transition networks but has not yet been used for reconstruction of GRNs. We implemented Friedman's Bayesian Information Criterion (BIC) score function, modified K2 algorithm to learn Dynamic Bayesian Network structure with the score function and tested the performance of the algorithm for GRN reconstruction with synthetic time series gene expression data generated by GeneNetWeaver and real yeast benchmark experiment data.
  
  
  RESULTS
  We implemented an algorithm for DBN structure learning with Friedman's score function, tested it on reconstruction of both synthetic networks and real yeast networks and compared it with REVEAL in the absence or presence of preprocessed network generated by Zou&Conzen's algorithm. By introducing a stationary correlation between two consecutive time slices, Friedman's score function showed a higher precision and recall than the naive REVEAL algorithm.
  
  
  CONCLUSIONS
  Friedman's score metrics for DBN can be used to reconstruct transition networks and has a great potential to improve the accuracy of gene regulatory network structure prediction with time series gene expression datasets.
authors.affiliation: School of Computing, University of Southern Mississippi, Hattiesburg, MS 39406, USA.
authors.forename: Haoni
authors.initials: H
authors.lastname: Li
authors.forename: Nan
authors.initials: N
authors.lastname: Wang
authors.forename: Ping
authors.initials: P
authors.lastname: Gong
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Perkins
authors.forename: Chaoyang
authors.initials: C
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism