RaPiDS: an algorithm for rapid expression profile database search.
In this paper we present a fast algorithm and implementation for computing the Spearman rank correlation (SRC) between a query expression profile and each expression profile in a database of profiles. The algorithm is linear in the size of the profile database with a very small constant factor. It is designed to efficiently handle multiple profile platforms and missing values. We show that our specialized algorithm and C++ implementation can achieve an approximately 100-fold speed-up over a reasonable baseline implementation using Perl hash tables. RaPiDS is designed for general similarity search rather than classification - but in order to attempt to classify the usefulness of SRC as a similarity measure we investigate the usefulness of this program as a classifier for classifying normal human cell types based on gene expression. Specifically we use the k nearest neighbor classifier with a t statistic derived from SRC as the similarity measure for profile pairs. We estimate the accuracy using a jackknife test on the microarray data with manually checked cell type annotation. Preliminary results suggest the measure is useful (64% accuracy on 1,685 profiles vs. the majority class classifier's 17.5%) for profiles measured under similar conditions (same laboratory and chip platform); but requires improvement when comparing profiles from different experimental series.
Horton
Paul B
PB
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. horton-p@aist.go.jp
Kiseleva
Larisa
L
Fujibuchi
Wataru
W
D000465:Algorithms; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*