Novel Affymetrix GeneChip Arrays:
Large-Scale Data Visualization and Analysis
SGTC scientists have developed novel DNA chips including genome tiling and splice junction designs. While these chips are scanned by standard Affymetrix protocols, custom processing and analysis is needed for the volume of data on these chips (see automation of data collection and storage at the SGTC).
Tiling chips present unique opportunities for genome analysis, since the entire genomic sequence is present on the chip, not just annotated coding regions. However, experiments yielding >6,000,000 data pts/experiment are not easily interpreted, and adaptable and extensible software tools are required for analysis and visualization of custom chip data.
Building on experience with data analysis and visualization with the A. thaliana chips we are adapting existing tools for use with our custom chip data and developing new software applications. Available tools, such as genome browsers and expression chip analysis software are used with our custom data sets. Scripts are written as needed to provide appropriate input files of our data for the programs. We have also written a set of JAVA applications for custom analysis and display for data unique to our custom Arabidopsis thaliana DNA chips.
Personnel
Ron Davis
Curtis Palm
Impact/Significance
Data processing protocols for initial chip analysis
Visualization & analysis tools for custom tiling chips
Accomplishments
Custom JAVA visualization and analysis tools for A. thaliana chips
Integration of A. thaliana data in genome browsers
genome Technology Center 
SGTC scientists have developed novel DNA chips including genome tiling and splice junction designs. While these chips are scanned by standard Affymetrix protocols, custom processing and analysis is needed for the volume of data on these chips (see automation of data collection and storage at the SGTC).