Figure 5.

Reanalysis of the Stamper microarray dataset. (A) Clustering of craniosynostosis samples by overall similarity (as in Figure 2) shows 4 clusters of samples. Colors to the left indicate the technical clusters observed in the raw data Additional file 1: Suppl. Figure 2), and indicate that this effect has been effectively removed by the SNM normalization procedure. (B) Two-way hierarchical clustering of 2883 probes significantly different in any pairwise contrast at NLP10 tends to recapitulate the four clusters. Each row is a sample, and column a transcript, and most of the rows are clustered with respect to the assignments in (A). The plot also clearly indicates genes that are specifically up regulated or down regulated in each cluster type. (C) Heat map of standardized least square means of genes within the four cluster types.