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Issue 7, 2013
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A methodology to infer gene networks from spatial patterns of expression – an application to fluorescence in situ hybridization images

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Abstract

The proper functional development of a multicellular organism depends on an intricate network of interacting genes that are expressed in accurate temporal and spatial patterns across different tissues. Complex inhibitory and excitatory interactions among genes control the territorial differences that explain specialized cell fates, embryo polarization and tissues architecture in metazoans. Given the nature of the regulatory gene networks, similarity of expression patterns can identify genes with similar roles. The inference and analysis of the gene interaction networks through complex network tools can reveal important aspects of the biological system modeled. Here we suggest an image analysis pipeline to quantify co-localization patterns in in situ hybridization images of Drosophila embryos and, based on these patterns, infer gene networks. We analyze the spatial dispersion of the gene expression and show the gene interaction networks for different developmental stages. Our results suggest that the inference of developmental networks based on spatial expression data is biologically relevant and represents a potential tool for the understanding of animal development.

Graphical abstract: A methodology to infer gene networks from spatial patterns of expression – an application to fluorescence in situ hybridization images

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Publication details

The article was received on 27 Oct 2012, accepted on 21 Mar 2013 and first published on 22 Mar 2013


Article type: Paper
DOI: 10.1039/C3MB25475E
Citation: Mol. BioSyst., 2013,9, 1926-1930
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    A methodology to infer gene networks from spatial patterns of expression – an application to fluorescence in situ hybridization images

    M. G. Campiteli, C. H. Comin, L. D. F. Costa, M. M. Babu and R. M. Cesar, Mol. BioSyst., 2013, 9, 1926
    DOI: 10.1039/C3MB25475E

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