computational selection of transcriptomics experiments improves guilt-by-association analyses计算选择转录组实验提高了牵连分析.pdfVIP

Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses 1,2,3 2,3 ´ ´ ¨ 1,3 1,3 2,3 Prajwal Bhat , Haixuan Yang , Laszlo Bogre , Alessandra Devoto *, Alberto Paccanaro * 1 School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom, 2 Department of Computer Science, Royal Holloway University of London, Egham, United Kingdom, 3 Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom Abstract The Guilt-by-Association (GBA) principle, according to which genes with similar expression profiles are functionally associated, is widely applied for functional analyses using large heterogeneous collections of transcriptomics data. However, the use of such large collections could hamper GBA functional analysis for genes whose expression is condition specific. In these cases a smaller set of condition related experiments should instead be used, but identifying such functionally relevant experiments from large collections based on literature knowledge alone is an impractical task. We begin this paper by analyzing, both from a mathematical and a biological point of view, why only condition specific experiments should be used in GBA functional analysis. We are able to show that this phenomenon is independent of the functional categorization scheme and of the organisms being analyzed. We then present a semi-supervised algorithm that can select functionally relevant experiments from large collections of transcriptomics experiments. Our algorithm is able to select experiments relevant to a given GO term, MIPS FunCat