A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosohpila Blastoderm
Charless Fowlkes, Cris Luengo, Soile Keränen, Gunther Weber, Oliver Rübel, Min-Yu, Huang, Sohail Chatoor, Lisa Simirenko, Angela DePace, Clara, Henriquez, Amy Beaton, Richard Weiszmann, Susan Celniker, Bernd Hamann, David Knowles, Mark Biggin, Michael Eisen, Jitendra Malik
icon To fully understand animal transcription networks, it is essential to accurately measure the spatial and temporal expression patterns of transcription factors and their targets. We describe a registration technique that takes image-based data from hundreds of Drosophila blastoderm embryos, each costained for a reference gene and one of a set of genes of interest, and builds a model VirtualEmbryo. This model captures in a common framework the average expression patterns for many genes in spite of significant variation in morphology and expression between individual embryos. We establish the method's accuracy by showing that relationships between a pair of genes' expression inferred from the model are nearly identical to those measured in embryos costained for the pair. We present a VirtualEmbryo containing data for 95 genes at six time cohorts. We show that known gene-regulatory interactions can be automatically recovered from this data set and predict hundreds of new interactions.

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Charless Fowlkes, Cris Luengo Hendriks, Soile Keränen, Gunther Weber, Oliver Rübel, Min-Yu, Huang, Sohail Chatoor, Lisa Simirenko, Angela DePace, Clara, Henriquez, Amy Beaton, Richard Weiszmann, Susan Celniker, Bernd Hamann, David Knowles, Mark Biggin, Michael Eisen, and Jitendra Malik. A quantitative spatiotemporal atlas of gene expression in the drosohpila blastoderm. Cell, 133:364–374, 2008.

BibTeX Reference

    AUTHOR = {Fowlkes, Charless and Luengo Hendriks, Cris and Ker{\"a}nen, Soile and Weber, Gunther and R{\"u}bel, Oliver and Huang, Min-Yu, and Chatoor, Sohail and Simirenko, Lisa and DePace, Angela and Henriquez, Clara, and Beaton, Amy and Weiszmann, Richard and Celniker, Susan and Hamann, Bernd and Knowles, David and Biggin, Mark and Eisen, Michael and Malik, Jitendra},
    TITLE = "A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosohpila Blastoderm",
    JOURNAL = "Cell",
    YEAR = "2008",
    VOLUME = "133",
    PAGES = "364-374",
    TAG = "biological_images"