title: Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data.
abstract: BACKGROUND
  Many ChIP-Seq experiments are aimed at developing gold standards for determining the locations of various genomic features such as transcription start or transcription factor binding sites on the whole genome. Many such pioneering experiments lack rigorous testing methods and adequate 'gold standard' annotations to compare against as they themselves are the most reliable source of empirical data available. To overcome this problem, we propose a self-consistency test whereby a dataset is tested against itself. It relies on a supervised machine learning style protocol for in silico annotation of a genome and accuracy estimation to guarantee, at least, self-consistency.
  
  
  RESULTS
  The main results use a novel performance metric (a calibrated precision) in order to assess and compare the robustness of the proposed supervised learning method across different test sets. As a proof of principle, we applied the whole protocol to two recent ChIP-Seq ENCODE datasets of STAT1 and Pol-II binding sites. STAT1 is benchmarked against in silicodetection of binding sites using available position weight matrices. Pol-II, the main focus of this paper, is benchmarked against 17 algorithms for the closely related and well-studied problem of in silico transcription start site (TSS) prediction. Our results also demonstrate the feasibility of in silico genome annotation extension with encouraging results from a small portion of annotated genome to the remainder.
  
  
  BACKGROUND
  Available fromhttp://www.genomics.csse.unimelb.edu.au/gat.
authors.affiliation: National ICT Australia, Victoria Research Laboratories, The University of Melbourne, VIC 3010, Australia. justin.bedo@nicta.com.au
authors.forename: Justin
authors.initials: J
authors.lastname: Bedo
authors.forename: Adam
authors.initials: A
authors.lastname: Kowalczyk
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004257:DNA Polymerase II / Q000378:metabolism*; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D011401:Promoter Regions, Genetic; D050794:STAT1 Transcription Factor / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012984:Software; D024363:Transcription Initiation Site
chemical_list: D050794:STAT1 Transcription Factor; C494079:STAT1 protein, human; D004257:DNA Polymerase II