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The Flexible matriXarray Chip System: A New Perspective,,,for Probe Optimization in Gene-Expression Profiling

und correction and normalization between the tissues via housekeeping genes was calculated. To demonstrate the approach, the resulting probe profiles of one gene for each tissue are displayed in Figure 3.

The comparison of probe profiles reveals the similar behavior of some probes, while others show distinct differences. For the brain-specific gene (GenBank acc. no. AB049056), all five probes show the same tendency; however, probes 3 and 4 display the most preferred pattern due to their high degree of profile similarity and specificity for the brain tissue. Representing the liver-specific gene (GenBank acc. no. J02585), probes 2, 5, and 6 display similar attributes; however, especially probes 4 and 7 show a more distinct pattern (a high signal in brain and/or kidney and a lower signal in liver compared to the other probes), indicating a dysfunction of these two probes. For the kidney- specific gene (GenBank acc. no. AF062389), probes 2, 5, 6, and 7 seem to be specific, while probes 1, 3, and 4 show aberrations in their intensity pattern.

In an ongoing study, the expression levels of 130 genes in 5 different human tissues are analyzed. The goal of this study is to establish an automated workflow for probe selection.

Fast and Convenient Iteration of Chip Layout

In conclusion, the data shown here demonstrate the impact of experimental probe validation in gene-expression profiling experiments. Based on the high flexibility in the production of customized chips, the matriXarray Chip System is the first platform that allows a fast and convenient iteration of chip layouts. Since probe optimization is crucial for all microarray applications, future work will extend this approach to applications outside of ex
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