Genetics, Vol. 162, 2037-2047, December 2002, Copyright © 2002
BEST: A Novel Computational Approach for Comparing Gene Expression Patterns From Early Stages of Drosophila melanogaster Development
Sudhir Kumara,b,
Karthik Jayaramanc,
Sethuraman Panchanathana,c,d,
Rajalakshmi Gurunathana,d,
Ana Marti-Subiranae, and
Stuart J. Newfeldb
a Center for Evolutionary Functional Genomics, Arizona State University, Tempe, Arizona 85287
b Department of Biology, Arizona State University, Tempe, Arizona 85287
c Department of Electrical Engineering, Arizona State University, Tempe, Arizona 85287
d Department of Computer Science and Engineering, Arizona State University, Tempe, Arizona 85287
e Phoenix College, Phoenix, Arizona 85013
Corresponding author:
Sudhir Kumar, Life Sciences Center A-351, Arizona State University, Tempe, AZ 85287-1501., s.kumar{at}asu.edu (E-mail)
Communicating editor: S. YOKOYAMA
Embryonic gene expression patterns are an indispensable part of modern developmental biology. Currently, investigators must visually inspect numerous images containing embryonic expression patterns to identify spatially similar patterns for inferring potential genetic interactions. The lack of a computational approach to identify pattern similarities is an impediment to advancement in developmental biology research because of the rapidly increasing amount of available embryonic gene expression data. Therefore, we have developed computational approaches to automate the comparison of gene expression patterns contained in images of early stage Drosophila melanogaster embryos (prior to the beginning of germ-band elongation); similarities and differences in gene expression patterns in these early stages have extensive developmental effects. Here we describe a basic expression search tool (BEST) to retrieve best matching expression patterns for a given query expression pattern and a computational device for gene interaction inference using gene expression pattern images and information on the associated genotypes and probes. Analysis of a prototype collection of Drosophila gene expression pattern images is presented to demonstrate the utility of these methods in identifying biologically meaningful matches and inferring gene interactions by direct image content analysis. In particular, the use of BEST searches for gene expression patterns is akin to that of BLAST searches for finding similar sequences. These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks.
