similarity queries for temporal toxicogenomic expression profiles相似性查询时间toxicogenomic表达谱.pdfVIP

Similarity Queries for Temporal Toxicogenomic Expression Profiles 1,2 3 3 1,2 Adam A. Smith *, Aaron Vollrath , Christopher A. Bradfield , Mark Craven 1 Department of Computer Science, University of Wisconsin, Madison, Wisconsin, United States of America, 2 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America, 3 Department of Oncology, University of Wisconsin, Madison, Wisconsin, United States of America Abstract We present an approach for answering similarity queries about gene expression time series that is motivated by the task of characterizing the potential toxicity of various chemicals. Our approach involves two key aspects. First, our method employs a novel alignment algorithm based on time warping. Our time warping algorithm has several advantages over previous approaches. It allows the user to impose fairly strong biases on the form that the alignments can take, and it permits a type of local alignment in which the entirety of only one series has to be aligned. Second, our method employs a relaxed spline interpolation to predict expression responses for unmeasured time points, such that the spline does not necessarily exactly fit every observed point. We evaluate our approach using expression time series from the EDGE toxicology database. Our experiments show the value of using spline representations for sparse time series. More significantly, they show that our time warping method provides more accurate alignments and classifications than previous standard alignment methods for time series. Citation: Smith AA, Vollrath A, Bradfield CA, Craven M (2008) Similarity Queries for Temporal Toxicogenomic Expression Profiles. PLoS Comput Biol 4(7):