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figures
Figure 1: Sample graph of expression data from GeneSpring®
Figure 2: Sample of a Venn diagram from GeneSpring®
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microarray hardware The facility currently houses a Genomics Solutions GeneTac BioChip System consisting of a Flexys Robotic Workstation for sample arraying and a GeneTac Hybridization Station, as well as a Perkin Elmer Scan Array Express HT®
software available The Perkin Elmer Scan Array Express HT® Scanner includes the ScanArray® software package. With this software the user can import or design new array templates, set up scan protocols for individuals or an entire group, perform basic statistical analysis and normalization as well as basic quantitation of expression data. Unlike other software in the same class, composite images of Cy3 and Cy5 scans can be easily created and exported for publication. The ScanArray® software is user friendly and works with image files created from all other commercial scanners. We also have two copies of ArrayVision® available for use. The features included with ArrayVision® are very similar to ScanArray®, however this program is less intuitive and can be somewhat laborious for the inexperienced user. By far the most robust of the microarray analysis programs we currently have available is the GeneSpring® program from Silicon Genetics. With GeneSpring® users can normalize data, compare data from dye swap experiments and run a variety of statistical analyses including student T-test and ANOVA to fit any type of data set. An interesting feature of GeneSpring® is the script building and editing capability used to automate analysis of large groups of data. Expression data can be analyzed and presented in a variety of easily exported formats, including 3D scatter plots, Venn diagrams and histograms. Large groups of data can also be saved and analyzed as smaller "experiments" based on such things as gene family or function. In addition, genes from scanned and analyzed data can be visualized based on location within a pathway with enzyme numbers linked directly to available online databases. Researchers interested in using any of these programs should contact allison-gillaspy@ouhsc.edu directly to set up an appointment.
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