rbf-tss identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequenciesrbf-tss转录开始网站的识别在人类使用径向基函数网络和寡核苷酸位置频率.pdfVIP

RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies Rami N. Mahdi, Eric C. Rouchka* Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America Abstract Accurate identification of promoter regions and transcription start sites (TSS) in genomic DNA allows for a more complete understanding of the structure of genes and gene regulation within a given genome. Many recently published methods have achieved high identification accuracy of TSS. However, models providing more accurate modeling of promoters and TSS are needed. A novel identification method for identifying transcription start sites that improves the accuracy of TSS recognition for recently published methods is proposed. This method incorporates a metric feature based on oligonucleotide positional frequencies, taking into account the nature of promoters. A radial basis function neural network for identifying transcription start sites (RBF-TSS) is proposed and employed as a classification algorithm. Using non- overlapping chunks (windows) of size 50 and 500 on the human genome, the proposed method achieves an area under the Receiver Operator Characteristic curve (auROC) of 94.75% and 95.08% respectively, providing increased performance over existing TSS prediction methods. Citation: Mahdi RN, Rouchka EC (2009) RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies. PLoS ONE 4(3): e4878. doi:10.1371/journal.pone.0004878 Editor: Darren P. Martin, Institute of Infectious Disease and Molecular Medicine, South Africa Received October 23, 2008; Accepted February 20, 2009; Published March 16, 2009 Copyright: 20