A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. Academic Article uri icon


  • BACKGROUND: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions. RESULTS: We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/. CONCLUSIONS: Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.

published proceedings

  • BMC Bioinformatics

altmetric score

  • 1

author list (cited authors)

  • Zhang, W., Feng, D., Li, R., Chernikov, A., Chrisochoides, N., Osgood, C., ... Ji, S.

citation count

  • 8

complete list of authors

  • Zhang, Wenlu||Feng, Daming||Li, Rongjian||Chernikov, Andrey||Chrisochoides, Nikos||Osgood, Christopher||Konikoff, Charlotte||Newfeld, Stuart||Kumar, Sudhir||Ji, Shuiwang

publication date

  • December 2013