title: Annotating gene function by combining expression data with a modular gene network.
abstract: BACKGROUND
  A promising and reliable approach to annotate gene function is clustering genes not only by using gene expression data but also literature information, especially gene networks.
  
  
  RESULTS
  We present a systematic method for gene clustering by combining these totally different two types of data, particularly focusing on network modularity, a global feature of gene networks. Our method is based on learning a probabilistic model, which we call a hidden modular random field in which the relation between hidden variables directly represents a given gene network. Our learning algorithm which minimizes an energy function considering the network modularity is practically time-efficient, regardless of using the global network property. We evaluated our method by using a metabolic network and microarray expression data, changing with microarray datasets, parameters of our model and gold standard clusters. Experimental results showed that our method outperformed other four competing methods, including k-means and existing graph partitioning methods, being statistically significant in all cases. Further detailed analysis showed that our method could group a set of genes into a cluster which corresponds to the folate metabolic pathway while other methods could not. From these results, we can say that our method is highly effective for gene clustering and annotating gene function.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan.
authors.forename: Motoki
authors.initials: M
authors.lastname: Shiga
authors.forename: Ichigaku
authors.initials: I
authors.lastname: Takigawa
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mamitsuka
mesh_terms: D001185:Artificial Intelligence; D030541:Databases, Genetic; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods; D010506:Periodicals as Topic; D020543:Proteome / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D018511:Systems Integration
chemical_list: D020543:Proteome