Figure 3

Isomap analysis of the rat multiple tissue gene expression data set. Three- and two-dimensional Isomap models were generated from a data set containing 122 samples from 11 peripheral tissues, 15 brain regions of three common out-bred rat strains, such as Wistar, Wistar Kyoto, and Sprague Dawley as described in Systems and Methods. Panel A shows an overview of a two-dimensional model using k = 3 nearest neighbors. Panel B shows the residual variance after the application of Isomap, MDS, and PCA models. Panel C shows a 2-dimensional comparison map generated by Principal Component Analysis. This panel demonstrates that PCA, unlike Isomap, is less accurate in mapping the different tissues correctly. Arrows show that (1) the skeletal muscle and kidney samples are overlapping the forebrain samples, (2) the thymus and spleen samples overlap the nucleus accumbens samples, and (3) the small intestine samples are mapped at a distance from the (4) large intestine samples. Panel D shows a portion of panel A with a three-dimensional model with k = 4. Panel E presents another region of the overview map representing the central brain structures. The neighborhood graphs demonstrate the k = 3 nearest neighbors. Panel F presents the anatomic locations of the samples on brain slice images from the Neuroscience Division, Regional Primate Research Center, University of Washington: BrainInfo (2000) http://braininfo.rprc.washington.edu. The abbreviations are: A, amygdala; ACN, amygdala central nucleus; CMFC, cortex minus frontal cortex; DR, dorsal raphe; DRGF, Fisher dorsal root ganglia; DS, dorsal striatum; endoth, endothel; FC, frontal cortex; H, hypothalamus; LIntestine, large intestine; LocCer, locus ceruleus; NAccumb, nucleus accumbens; PCN, primary cortical neurons; PFC, prefrontal cortex; Pineal, pineal gland; Pituit, pituitary gland; SIntestine, small intestine; SkelMusc, skeletal muscle; Thym, thymus; VS, ventral striatum; and VTA, ventral tegmental area. See text for more detail.