Figure 3

Analysis of gene expression time series data during the onset of liver regeneration. (A) Cluster analysis of the differential expression temporal profiles. The data was clustered using Partitioning Around Medoids using Pearson Correlation as the distance metric and with k = 6 (optimal number obtained from the results shown in Figure 1). Each row corresponds to a gene and each column corresponds to one of the four time points (1, 2, 4, 6 hours post partial hepatectomy). Lines demarcate the cluster boundaries. (B) The six clusters from (A) were analyzed for over-represented TF binding sites in the corresponding promoters using PAINT. The representative interaction matrix is shown. The rows represent the promoters and columns represent TFs. Each binding site for a TF on a promoter is marked red or grey, depending whether the frequency of that binding site in that cluster is statistically significantly overrepresented or not, respectively. Binding sites for several TFs known to be relevant in liver development and regeneration are enriched in distinct expression clusters. Lines indicate the mapping between the gene groups in the expression map and the corresponding promoter sets in the regulatory interaction matrix.