title: An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae.
abstract: BACKGROUND
  Probabilistic functional gene networks are powerful theoretical frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems. Such networks provide syntheses of millions of discrete experimental observations, spanning DNA microarray experiments, physical protein interactions, genetic interactions, and comparative genomics; the resulting networks can then be easily applied to generate testable hypotheses regarding specific gene functions and associations.
  
  
  RESULTS
  We report a significantly improved version (v. 2) of a probabilistic functional gene network of the baker's yeast, Saccharomyces cerevisiae. We describe our optimization methods and illustrate their effects in three major areas: the reduction of functional bias in network training reference sets, the application of a probabilistic model for calculating confidences in pair-wise protein physical or genetic interactions, and the introduction of simple thresholds that eliminate many false positive mRNA co-expression relationships. Using the network, we predict and experimentally verify the function of the yeast RNA binding protein Puf6 in 60S ribosomal subunit biogenesis.
  
  
  CONCLUSIONS
  YeastNet v. 2, constructed using these optimizations together with additional data, shows significant reduction in bias and improvements in precision and recall, in total covering 102,803 linkages among 5,483 yeast proteins (95% of the validated proteome). YeastNet is available from http://www.yeastnet.org.
authors.affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Insuk
authors.initials: I
authors.lastname: Lee
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Li
authors.forename: Edward M
authors.initials: EM
authors.lastname: Marcotte
mesh_terms: D005189:False Positive Reactions; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D011336:Probability; D025941:Protein Interaction Mapping; D040901:Proteomics / Q000379:methods; D012333:RNA, Messenger / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000502:physiology*
chemical_list: D012333:RNA, Messenger