Eric LeProust

Light-directed, programmable microarray synthesis

DNA Microarrays have become important in genome-wide expression studies. However, to fully use the power of the microarrays, more sophisticated and userfriendly data management and analysis tools have to be developed. We have developed a software package called MAT (Microarray Analysis Tools). MAT consists of a data entry tool, a web-based analysis tool and a relational database. User interfaces written in Java and JDBC are used to access the relational database (Sybase Adaptive server 11.5). The data entry tool is a form-based interface for user-friendly data entry. The web-based analysis tools consist of a synthetic image view tool, a graphic plot tool to display results from a series of experiments and a neural network-based data clustering tool. All of the interfaces are inter-connected. A user can view a single experiment or multiple experiments. A user can plot a time course, as well as a correlation graph with different experimental conditions. The mouse and human clone databases are automatically updated by searching through GenBank. The program also allows for the user to obtain GenBank data for any clone. Finally, the cluster tool will provide an advanced algorithm for clustering selected data. Our MAT tools are facilitating gene expression studies at AECOM, and can be adapted for use in other research laboratories.