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Informatics Framework for Analysis of Development and Differentiation at CBIL
The Computational Biology and Informatics Laboratory (CBIL) group at Penn has built an informatics framework designed for the functional analysis of development and differentiation at the cellular level. Given the information provided through various genome and EST (expressed sequence tag) sequencing projects, it is now possible to characterize comprehensively the molecular phenotype of cells during development and differentiation. This information will drive deeper understanding of both normal and abnormal developmental processes. The system combines data management and visualization facilities with automated and manual data analysis components. Integral to the system is the Genomics Unified Schema (GUS) based upon the central dogma of biology (DNA -> RNA -> protein) that incorporates several CBIL prototype databases. The power of GUS is the ability to provide system-specific views of integrated information at the DNA, RNA, and protein levels using a common set of tools. These views may be tissue-specific such as described recently for hematopoietic stem cells (Phillips et al., The Genetic Program of Hematopoietic Stem Cells, Science 288:1635-40, 2000), or they may be organism-specific such as PlasmodiumDB, the central repository for data generated by the Malaria Genome Consortium. The RNA Abundance Database developed by IME Member Chris Stoeckert is a gene expression database containing results from high throughput methods and represents an indication of future directions. Through RAD, data are currently incorporated into this informatics framework from emerging technologies such as microarrays.
