Biological data integration : towards a global understanding of ascadian development

The growing complexity of biological questions and the exponential increase in available data to explore these questions are making the management and integration of such information a serious issue for a successful research activity. I therefore aimed at exploring how data integration techniques could be used to answer complex biological problems. In this context, the ANISEED database emerged as an ideal data integration platform, given its rich representation of concepts related to organism development, the availability of large volumes of multiple types of experimental data and the relative simplicity of the ascidian model system. I thus used this rich resource to explore complex biological questions: 1) is the chordate body plan found both in ascidians and vertebrates the result of a common genetic program? By systematically comparing all available gene expression patterns from ANISEED and ZFIN (for zebrafish) I observed a generalized divergence in the gene expression programs of both species, with some similarity noticeable in the locomotory system; 2) what are the gene regulatory networks underlying ascidian development? By formalizing simple rules used by researchers to infer gene regulatory events, I was able to automatically recover, from the experimental data available in ANISEED, a network of gene regulatory interactions throughout ascidian development. These simple examples may indicate potential paths towards the use of data integration in Biology.