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Fig. 3. Expression profiling analysis of transdetermining cells. Cluster analysis of eight different comparisons. Expression ratios are color coded as indicated. Each of 35 columns represents an array experiment grouped into categories as described in Table S1 (see supplementary material). Categories 4, 5 and 5 compare TD cells with D_Wg, V_Wg and D_WT, respectively. Prior to cluster analysis, the expression ratios were filtered at two levels: (1) spots were required to have intensities with a sum of medians greater than 350; and (2) ratios greater than 2 (1 log₂) in at least five out of the 35 experiments. The calculation of self-organizing maps and hierarchical clustering produced a cluster with several sub-clusters, of which six are represented; labeled I-VI with I-IV including genes enriched in TD cells and V and VI containing genes depleted in TD cells. Genes that segregate to sub-cluster I had high levels of expression in TD cells (yellow) and include lama and CG14059. The many absent calls (grey) in the wing-to-leg comparison for genes of this sub-cluster suggest that these genes are not expressed in either wild-type wing or leg discs, but are enriched in Wg-induced leg discs undergoing transdetermination. Genes in subclusters II and III also had elevated expression in TD cells, but do not have elevated expression levels in wing discs. Subcluster II includes CG12534. Genes that segregated to subcluster IV show high expression in wing discs (yellow) and some of these genes are enriched in TD cells, indicating the realization of a wing developmental program in Wg-induced leg discs. This group includes ap and vg. Genes in subclusters V and VI are expressed at low levels in the TD cell preparation (blue). Components of the Notch signaling pathway and the PcG gene Su(z)2 are included in this group. Gene names for all genes are listed in Tables S7 and S8 (see supplementary material). Some genes are represented by replicate spots on the microarray, causing multiple listings.

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