title: Comparison of computational methods for the identification of cell cycle-regulated genes.
abstract: BACKGROUND
  DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been subjected to a wide range of bioinformatics analysis methods, aimed at identifying the correct and complete set of periodically expressed genes.
  
  
  RESULTS
  Here, we provide the first thorough benchmark of such methods, surprisingly revealing that most new and more mathematically advanced methods actually perform worse than the analysis published with the original microarray data sets. We show that this loss of accuracy specifically affects methods that only model the shape of the expression profile without taking into account the magnitude of regulation. We present a simple permutation-based method that performs better than most existing methods.
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark DK-2800 Lyngby, Denmark.
authors.forename: Ulrik
authors.initials: U
authors.lastname: de Lichtenberg
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.forename: Anders
authors.initials: A
authors.lastname: Fausbøll
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Jensen
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
mesh_terms: D000465:Algorithms; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D018816:Genes, cdc / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D018797:Cell Cycle Proteins; D029701:Saccharomyces cerevisiae Proteins