Figure 2

Clustering and functional analysis of mRNA and total regulatory load profiles. k-means clustering was used to summarize the main patterns of mRNA levels (A) and total regulatory load (B) across the regeneration profile. Within each cluster we identified enriched pathways and functions. The numbers on the left of each cluster indicate the cluster number (referenced in Additional files 5 and 6) and the number of genes in the cluster. Contrasting the mRNA expression levels with the total regulatory load (TRL) for a set of genes in an enriched pathway reveals information about the potential effect of miRNA regulation. Genes in (C) and (D) display different regulatory relationships. Panel C contains genes for which increased TRL precedes or coincides with decreased overall expression of immediately early (Fos) or antiproliferative target genes (GAS1 and SPHK2), whereas in Panel D, containing genes involved in the DNA replication checkpoint pathway, the TRL (dashed lines) begins to increase at 36 hours posthepatectomy (S phase peak), 12 hours prior to the increase of the relevant mRNAs (solid lines).