title: Plant promoter prediction with confidence estimation.
abstract: Accurate prediction of promoters is fundamental to understanding gene expression patterns, where confidence estimation is one of the main requirements. Using recently developed transductive confidence machine (TCM) techniques, we developed a new program TSSP-TCM for the prediction of plant promoters that also provides confidence of the prediction. The program was trained on 132 and 104 sequences and tested on 40 and 25 sequences (containing TATA and TATA-less promoters, respectively) with known transcription start sites (TSSs). As negative training samples for TCM learning we used coding and intron sequences of plant genes annotated in the GenBank. In the test set of TATA promoters, the program correctly predicted TSS for 35 out of 40 (87.5%) genes with a median deviation of several base pairs from the true site location. For 25 TATA-less promoters, TSSs were predicted for 21 out of 25 (84%) genes, including 14 cases of 5 bp distance between annotated and predicted TSSs. Using TSSP-TCM program we annotated promoters in the whole Arabidopsis genome. The predicted promoters were in good agreement with the start position of known Arabidopsis mRNAs. Thus, TCM technique has produced a plant-oriented promoter prediction tool of high accuracy. TSSP-TCM program and annotated promoters are available at http://mendel.cs.rhul.ac.uk/mendel.php?topic=fgen.
authors.affiliation: Royal Holloway, University of London Egham, Surrey TW20 0EX, UK.
authors.forename: I A
authors.initials: IA
authors.lastname: Shahmuradov
authors.forename: V V
authors.initials: VV
authors.lastname: Solovyev
authors.forename: A J
authors.initials: AJ
authors.lastname: Gammerman
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D016001:Confidence Intervals; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
references.citation: Nat Genet. 2000 Oct;26(2):225-8
references.pmid: 11017083
references.citation: Science. 2002 Apr 5;296(5565):92-100
references.pmid: 11935018
references.citation: Bioinformatics. 2001;17 Suppl 1:S199-206
references.pmid: 11473010
references.citation: Genes Dev. 2000 Oct 15;14(20):2551-69
references.pmid: 11040209
references.citation: Genome Res. 2001 Mar;11(3):333-40
references.pmid: 11230158
references.citation: J Mol Biol. 2000 Mar 31;297(3):599-606
references.pmid: 10731414
references.citation: Genes Dev. 2001 Oct 1;15(19):2503-8
references.pmid: 11581155
references.citation: IEEE Trans Neural Netw. 1999;10(5):988-99
references.pmid: 18252602
references.citation: Comput Chem. 1999 Jun 15;23(3-4):191-207
references.pmid: 10404615
references.citation: Proc Int Conf Intell Syst Mol Biol. 1997;5:294-302
references.pmid: 9322052
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850
references.citation: Genome Res. 2002 Mar;12(3):458-61
references.pmid: 11875034
references.citation: Genes Dev. 1997 Nov 15;11(22):3020-31
references.pmid: 9367984
references.citation: Bioinformatics. 1999 May;15(5):362-9
references.pmid: 10366656
references.citation: Nature. 2000 Dec 14;408(6814):796-815
references.pmid: 11130711
references.citation: Bioinformatics. 2002 Jan;18(1):198-9
references.pmid: 11836231
references.citation: Genome Res. 1997 Sep;7(9):861-78
references.pmid: 9314492
references.citation: Bioinformatics. 1999 May;15(5):356-61
references.pmid: 10366655
references.citation: Science. 2002 Apr 5;296(5565):79-92
references.pmid: 11935017
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):114-7
references.pmid: 12519961
references.citation: Nature. 2002 Dec 5;420(6915):586-90
references.pmid: 12466855
references.citation: Trends Genet. 2001 Feb;17(2):56-60
references.pmid: 11173099
references.citation: Biochim Biophys Acta. 1997 Mar 20;1351(1-2):73-88
references.pmid: 9116046
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3540-5
references.pmid: 12824362
references.citation: Mamm Genome. 1999 Feb;10(2):168-75
references.pmid: 9922398