Figure 3

Distinct Significant Expression Profiles Clustered by STEM. A-H. Average fold change values for the genes in each cluster were plotted against the real time scale of the time-points post-injury. Error bars denote the standard deviation of the mean. Three classes of expression profiles are observed. Class I profiles (A-C) display an “up-down” pattern with the peak of up-regulation in 24 hours (profiles 45, 46 and 48) post-injury. The up-regulation is followed by decline of transcript levels, either sharply back to normal values (profiles 45 and 48) or gradually to higher than control values (profiles 46). Class II profiles (1 and 0) are quite similar to each other as they display down-regulations of many genes on day 1, which stay at lower than normal levels even at 8 weeks post-injury. Class III profiles (E-H) represent fluctuating profiles and are subdivided into two clusters. Cluster I (Profiles 44 and 41) is marked by an early increase in gene expression by day 1 followed by sudden decline in transcript level at day 3. In profile 44, this transient change in transcription level is followed by an escalating condition whereby the same transcripts are again up-regulated by day 7 and stay at higher than control values until 8 weeks post-injury. In cluster II (profile 6), a reverse phenomenon is observed, where the early event is a sharp decrease in transcript level and a follow up fluctuation pattern in gene expression. Despite fluctuations in gene expression levels, the transcript levels of genes in profiles 6 remain significantly lower than control levels throughout the course of experiment.