title: High sensitivity TSS prediction: estimates of locations where TSS cannot occur.
abstract: BACKGROUND
  Although transcription in mammalian genomes can initiate from various genomic positions (e.g., 3'UTR, coding exons, etc.), most locations on genomes are not prone to transcription initiation. It is of practical and theoretical interest to be able to estimate such collections of non-TSS locations (NTLs). The identification of large portions of NTLs can contribute to better focusing the search for TSS locations and thus contribute to promoter and gene finding. It can help in the assessment of 5' completeness of expressed sequences, contribute to more successful experimental designs, as well as more accurate gene annotation.
  
  
  METHODS
  Using comprehensive collections of Cap Analysis of Gene Expression (CAGE) and other transcript data from mouse and human genomes, we developed a methodology that allows us, by performing computational TSS prediction with very high sensitivity, to annotate, with a high accuracy in a strand specific manner, locations of mammalian genomes that are highly unlikely to harbor transcription start sites (TSSs). The properties of the immediate genomic neighborhood of 98,682 accurately determined mouse and 113,814 human TSSs are used to determine features that distinguish genomic transcription initiation locations from those that are not likely to initiate transcription. In our algorithm we utilize various constraining properties of features identified in the upstream and downstream regions around TSSs, as well as statistical analyses of these surrounding regions.
  
  
  CONCLUSIONS
  Our analysis of human chromosomes 4, 21 and 22 estimates ∼46%, ∼41% and ∼27% of these chromosomes, respectively, as being NTLs. This suggests that on average more than 40% of the human genome can be expected to be highly unlikely to initiate transcription. Our method represents the first one that utilizes high-sensitivity TSS prediction to identify, with high accuracy, large portions of mammalian genomes as NTLs. The server with our algorithm implemented is available at http://cbrc.kaust.edu.sa/ddm/.
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Ulf
authors.initials: U
authors.lastname: Schaefer
authors.forename: Rimantas
authors.initials: R
authors.lastname: Kodzius
authors.forename: Chikatoshi
authors.initials: C
authors.lastname: Kai
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D016678:Genome / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D020407:Internet; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017450:Receptors, Opioid, mu / Q000235:genetics; D015203:Reproducibility of Results; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: C404943:Oprm protein, mouse; D017450:Receptors, Opioid, mu