HOPACH clustering and GenMAPP annotation of genes changed in both DRG and SCG during neurite outgrowth in vitro. (A) The cluster displays the averaged Affymetrix microarray data for 5 time points of DRG outgrowth (2, 5, 12, 24, and 40 hours) and 6 time points of SCG outgrowth (same as DRG plus 65 hour endpoint), for the 712 probe sets found to change more than 1.5 fold (p ≤ 0.05) in both datasets. Genes annotated along the left column are those also found in two or more of the in vivo regeneration studies (see Figure 2). Yellow indicates increased expression or probe intensity relative to the acutely dissected reference pool, while blue indicates decreased expression (log2 scale). Horizontal gray bars separate the first level clusters, and colored vertical bars along the right indicate the next level of sub-clusters. (B) MAPPFinder annotations of Gene Ontology categories represented in the first-level clusters, along with number of genes found in this cluster relative to the total number found in all three clusters for each category (all Z-scores > 2 and permuted-p ≤ 0.05). Terms in parentheses show related categories that were also significant. Terms in bold have a p-value ≤ 0.05 after adjustment for multiple hypothesis testing. In cases where annotations for first-level clusters also appeared in MAPPFinder annotation of the next level sub-clusters (with Z-scores > 2, permuted-p ≤ 0.05), those localizations to sub-clusters are indicated by an appropriately colored square. (C) Six nucleic-acid binding genes were detected by GenMAPP in a sub-cluster of (A) (marked by asterisk). These genes peak temporally earlier than most others in cluster 3. Ratio of expression change over time for these genes is color-coded as in (A).