Abstract

ANALYSIS OF GENE EXPRESSION IN MOOD DISORDERS BY DIFFERENT ALGORITHMS USING AFFYMETRIX MICROARRAYS

MP Vawter; H Tomita; S Evans; P Choudary; J Li; JH Meador-Woodruff; RM Myers; S Watson; H Akil; EG Jones; WE Bunney
Society for Neuroscience 32nd annual meeting. 2002.

Abstract

We have analyzed gene transcript abundance by microarray analysis in bipolar disorder type I patients (n = 9), major depressive disorder (n = 11) and compared to a control group matched for age, gender, and post mortem interval (n = 20). We used tissue from three brain regions, anterior cingulate and dorsolateral prefrontal cortices, and cerebellar cortex. Each sample was run in duplicate on Affymetrix U95A chips at 2 of 3 laboratories. We have generated analyses using dCHIP (Li and Wong, 2001) and MAS5 software for both paired and group analyses. Each approach yields different lists of significant genes due to probe-level analyses differences. As a result, we further examined gene expression in each patient as compared to that in the individual matched controls using several paired analyses from MAS5 and dCHIP. The same dataset was examined by a group approach and we compare the significance levels of each approach. We are investigating other probe level methods using Perfect Match minus chip background. http://biosun01.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf). The effect of gender, PMI, and age will be further evaluated in our dataset. Finally, transformation of the Affymetrix dataset by z-scores (Vawter MP et al., 2001) will be compared to the MAS5 and dCHIP results.