Fig. 8

Gene expression dynamics during dissociation and reaggregation. A Fuzzy clustering [51] of temporal expression profiles during dissociation and reaggregation. We chose 15 clusters to represent our data, determined by hierarchical clustering of normalized read counts of the five conditions using hclust in R (Additional file 20: Figure S7). We found subgroups of profiles with a decrease in expression until 4hR (clusters 12,15), early peaks and a flat curve during reaggregation (clusters 3,8,5,6,10), peaks at 1hR (clusters 4,14), decreasing expression during dissociation and increasing expression in reaggregation (clusters 1,11,13), strong ascending trends (clusters 10,5) and a peak at 4hD (clusters 7, 2, 9). Cluster cores have a membership value > 0.7 (pink) (Additional file 13: Table S10). Other membership values are shown as follows: membership value between 0.5 and 0.7 (blue), membership value < 0.5 (green). B Selected GO terms corresponding to Biological Processes found to be enriched for each core cluster as determined by topGO [4] (Additional file 11: Table S8C). Colored boxes indicate significant enrichment in a given term (adj p-avlue < 0.05). The dendrogram at the top was calculated by hierarchical clustering using hclust with Euclidian distance of the normalized read counts of genes qualifying as cluster core (membership value > 0.7). C Expression profile of genes involved in epithelia organization and cell adhesion in bilaterians (see also Fig. 1A). Expression of genes of the three polarity complexes decrease during dissociation and increase upon reaggregation. The expression of the gene coding for the basement membrane collagen was rather stable during the process, while the expression of integrin β2 increased at 4hD and became stable at 1hR. Genes involved in adherens junctions globally show a decrease in expression during dissociation and an increase around 1hR. Expression of the cytoskeleton component actin increased upon dissociation and decreased when reaggregation started. Finally, four of the Aggregation Factors (AFs) candidates (AF 1, 3, 4, 5) were downregulated during dissociation and upregulated during reaggregation (in particular AF3). In contrast, AF2 was downregulated during the entire process. NSW stands for natural condition which is the control condition, 1hD and 4hD correspond to 1 h and 4 h of dissociation (in CMFSW) respectively, 1hR and 3hR stand for 1 h and 3 h or reaggregation (in NSW) respectively. See Additional file 15: Table S11 for Standardized TPM and log2 Fold Change values