Similarity queries for temporal toxicogenomic expression profiles.
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.
Smith
Adam A
AA
Department of Computer Science, University of Wisconsin, Madison, Wisconsin, USA. aasmith@cs.wisc.edu
Vollrath
Aaron
A
Bradfield
Christopher A
CA
Craven
Mark
M
D000818:Animals; D030541:Databases, Genetic; D064420:Drug-Related Side Effects and Adverse Reactions / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D008099:Liver / Q000187:drug effects; D051379:Mice; D010363:Pattern Recognition, Automated / Q000379:methods; D016415:Sequence Alignment; D013997:Time Factors; D043922:Toxicogenetics / Q000379:methods*