Fig. 2
From: Cycles of gene expression and genome response during mammalian tissue regeneration
Changing Post-PH gene-expression patterns and comparison with sham-surgery samples. a Heat-map display of seven-set PAM-clustering results for transcripts that varied Post-PH gene-expression patterns (i.e., Set 3). The individually normalized relative post-PH transcript abundance (red, high; white, low) for each gene is shown. The seven PAM-clustering sets (Set 3.1 to Set 3.7 indicated by the color coding column to the left) are each grouped together with the comparative medoid at the top of each set and decreasing gene-expression similarity shown from top to bottom. Set 3 PAM-clustering subset name (column 1), number of genes per subset (column 2), and percentage genes per subset with a negative silhouette clustering score (column 3) are given. PAM-clustering sets with genes down-regulated (Set 3.1 to Set 3.3) and up-regulated (Set 3.4 to Set 3.7) post-PH are indicated by the brackets labeled I and II, respectively. b Silhouette-score distributions and averages for each PAM-clustering subset. c Transcript-abundance comparison between post-PH and post-sham samples at 1, 4, 10, 20 and 48 h. Genes are indicated as dots in the same order as in a. The post-PH/sham ratio is given in log2 scale (x axes). Positive (higher post-PH expression in red) and negative (higher post-sham expression in green) log2 scores are indicated as color gradients. Gene transcripts with post-PH and post-sham log2 RPKM quantifications less than 0 are not shown. d Predominant specific function of genes for each Set 3 PAM-clustering subset and number of genes per cluster included in the 124-gene Mus musculus KEGG cell-cycle pathway. Only the most representative GO term that is specific for an individual subset is listed. The full list of enriched GO terms is given in Additional file 6: Table S3