Pattern Discovery in Gene Regulation: Designing an Analysis Environment

S. M. Veretnik and B. R. Schatz

Interactions that determine cellular fate are exceedingly complex, can take place at different levels of gene regulation and involve a large number of components (such as genes, proteins). Wet lab biology has an inherent difficulty in considering multiple components within one experimental set-up. Thus, the individual experimental results may reflect the behavior of a sub-system and be missing some important information concerning interactions with other components. Computational tools can help in simultaneously analyzing many different pieces of biological knowledge from different data sources. Such tools will aid in comprehending the whole system (call, organism) as a function of all its components; this, in turn, will facilitate discovery of the global patterns in genetic regulation. The Worm Community System (WCS) which contains extensive knowledge from many different sources regarding model organism C. elegans, presents a suitable environment for development of the integrated analysis tools. Here we describe a working version of WCS and the strategies employed for the development of the global analysis tools within the System. The present paper deals with the construction of a highly interconnected information space (in the context of the problem) by introducing more sophisticated data objects representing knowledge about genetic regulation. We describe construction of the in-depth objects, development of the analysis tools and discuss the type of analysis feasible within such interconnected space. The analysis tools will serve as an ideal environment for dry biology experimentation and provide a context for wet experiments.

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