The goal of this research program was to develop functional genomics technologies, such as new high-throughput techniques to characterize gene expression, and apply them to basic and clinical research. Ultimately, it aimed to provide researchers with tools to generate global views of disease, which may uncover new disease targets for drug development.

The project included several sub-projects aimed at the development of new technologies. These included engineering activities such as automation of array fabrication and processing and the development of a new, configurable robotics system and adaptation of current arraying systems to increase throughput and reproducibility. The project also involved molecular aspects such as the development of a novel recombinational cloning vector for optimal cell array applications; optimization of baculoviral protein production and purification for protein arrays and identification of new markers and predictors for several tumour classifications and predictor sets for cardiovascular disease. Computational developments included the development of inter-relational datasets that allow identification of new protein-protein interaction networks through computational analysis and computational optimization of array design.

The project resulted in the development of novel array-based technologies as well as refinements to existing array technologies. Furthermore, the project added new array chips to the investigators’ existing chip collection and led to the development of new arrays, including protein arrays, transfected cell arrays and antibody arrays.

Functional genomics studies generate large amounts of data that require robust computational platforms. To address these needs, the investigators developed two Linux-based computational clusters and software to study gene expression, cell dynamics and protein-protein interactions.

The outcomes of this work were also collected in two new databases: the Online Human Predicted Interaction Database (OPHID), now called the I2D database, which predicts protein-protein interaction in the human interactome, and the HomologousDB database, used to determine the ancestral origins of related gene sequences.

In sum, this project refined existing functional genomics systems and launched new technologies that allow researchers to generate a more comprehensive portrait of cellular activities. Eventually, this may lead to the identification of specific molecular targets involved in disease progression.