Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs

  • Cyrus L. Harmon
  • Parvez Ahammad
  • Ann Hammonds
  • Richard Weiszmann
  • Susan E. Celniker
  • S. Shankar Sastry
  • Gerald M. Rubin
Conference paper

DOI: 10.1007/978-3-540-71681-5_37

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4453)
Cite this paper as:
Harmon C.L. et al. (2007) Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs. In: Speed T., Huang H. (eds) Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453. Springer, Berlin, Heidelberg

Abstract

Determining the precise spatial extent of expression of genes across different tissues, along with knowledge of the biochemical function of the genes is critical for understanding the roles of various genes in the development of metazoan organisms. To address this problem, we have developed high-throughput methods for generating images of gene expression in Drosophila melanogaster imaginal discs and for the automated analysis of these images. Our method automatically learns tissue shapes from a small number of manually segmented training examples and automatically aligns, extracts and scores new images, which are analyzed to generate gene expression maps for each gene. We have developed a reverse lookup procedure that enables us to identify genes that have spatial expression patterns most similar to a given gene of interest. Our methods enable us to cluster both the genes and the pixels that of the maps, thereby identifying sets of genes that have similar patterns, and regions of the tissues of interest that have similar gene expression profiles across a large number of genes.

Primary keyphrases: Genomic imaging, Gene expression analysis,Clustering.

Secondary keyphrases: Microarray data analysis, Imaginal discs.

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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Cyrus L. Harmon
    • 1
  • Parvez Ahammad
    • 2
  • Ann Hammonds
    • 1
  • Richard Weiszmann
    • 3
  • Susan E. Celniker
    • 3
  • S. Shankar Sastry
    • 2
  • Gerald M. Rubin
    • 1
  1. 1.Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 
  2. 2.Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720 
  3. 3.Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 

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