Figure 7

Distinct cell–ECM interactions during tissue formation are cell–culture and cell-type dependent. Volcano plots showing the significant p-value levels for each ECM remodeling related gene as a function of its expression fold-regulation on pcECM. Each gene fold-regulation was normalized first to its own sample housekeeping gene expression level, then to equivalent normalized expression of identical three-day cultures on plates to identify which expression is pcECM induced. These double normalized expressions were then used to compared between the three culture systems to generate the three volcano plots as indicated (hMSC vs. HUVECs monoculture, (a); co-culture vs. hMSCs, (b); and co-culture vs. HUVECs, (c). Positive fold-regulation values show upregulation in the first culture system of each comparison pair while negative values show downregulation (or upregulation in the second culture system compared). Green marked genes showed both high statistical significance (p < 0.00061 per individual T-test based on ANOVA with Tukey–Kramer’s post hoc correction) as well as |X| > 5 fold-regulation change. Red dots are statistically not significant (p > 0.05) but have considerable |X| > 5 fold-regulation change; Yellow dots have a considerable |X| > 5 fold-regulation change with p values smaller than 0.05 but larger than the Tukey-Kramer’s post hoc correction cut-off value. Grey dots represent genes that are not sufficiently up or down regulated, even if statistically significant. Detailed values and statistical comparison results for all genes appear in Supplementary Tables S1–S3. Only the green dotted groups (six gene clusters of significantly top regulated genes) were used for gene-set analyses and comparison between the different culture conditions.