BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development

Sudhir Kumar, Karthik Jayaraman, Sethuraman Panchanathan, Rajalakshmi Gurunathan, Ana Marti-Subirana, Stuart Newfeld

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2037-2047
Number of pages11
JournalGenetics
Volume162
Issue number4
StatePublished - Dec 1 2002

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Drosophila melanogaster
Gene Expression
Developmental Biology
Computational Biology
Genes
Drosophila
Embryonic Structures
Genotype
Research Personnel
Equipment and Supplies
Research

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

BEST : A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. / Kumar, Sudhir; Jayaraman, Karthik; Panchanathan, Sethuraman; Gurunathan, Rajalakshmi; Marti-Subirana, Ana; Newfeld, Stuart.

In: Genetics, Vol. 162, No. 4, 01.12.2002, p. 2037-2047.

Research output: Contribution to journalArticle

Kumar, Sudhir ; Jayaraman, Karthik ; Panchanathan, Sethuraman ; Gurunathan, Rajalakshmi ; Marti-Subirana, Ana ; Newfeld, Stuart. / BEST : A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. In: Genetics. 2002 ; Vol. 162, No. 4. pp. 2037-2047.
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