How complexity increases in development: An analysis of the spatial–temporal dynamics of 1218 genes in Drosophila melanogaster

• Quantitative analysis of gene expression complexity in Drosophila development.
• We use three mathematical measures of gene expression compartmentalization in space.
• All measures show a similar non-linear increase in compartmentalization over time.
• Transcription factors and growth factors showed an earlier compartmentalization.

One of the most apparent phenomena in development is that it starts with something apparently simple and leads to something clearly complex with a specific and functional structure. At the level of gene expression it seems also clear that the embryo becomes progressively compartmentalized over time and space. However, there have not been any systematic attempts to quantify how this occurs. Here, we present a quantitative analysis of the compartmentalization and spatial complexity of gene expression in Drosophila melanogaster over developmental time by analyzing thousands of gene expression spatial patterns from FlyExpress database. We use three different mathematical measures of compartmentalization of gene expression in space. All these measures show a similar non-linear increase in compartmentalization over time, with the most dramatic change occurring from the maternal to the early gastrula stage. Transcription factors and growth factors showed an earlier compartmentalization. Finally, we partitioned the embryo space in 257 equally sized regions and clustered them depending on their expression similarity, within and between stages. This provides a global overview about the effective degree of differentiation and compartmentalization between body parts at each developmental stage and when and where in the embryo there are more changes, due to signaling or movement.

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