Figure 4

Alignment of transcriptomes of two samples from a differentiation series of mesenchymal stem cells at the 0 h and 7d time-points. A) Alignments for the two time-points are visualized in reference to all normal tissue types. On the left side is a phylogenic tree of all the 44 normal tissue types in the reference database arranged according to their similarities in gene expression against one another. Colored lines connect the test samples to their six best tissue matches, with the thickness of the line reflecting the number of typical genes. B) Heatmaps illustrating the AGEP results at the 0 h timepoint. The upper heatmap shows the alignment against all genes in the six best-matching tissues arranged in the order of their tm-scores with the best matching tissue. Green color indicates that the gene has a typical and red color an atypical expression level for each tissue type. The two lower heatmaps show results specifically for adipocyte differentiation and lipid and fatty acid transport gene sets. The relative enrichment of the gene set members among tissue atypical genes is shown on the right. C) Alignment results at the 7d timepoint. The data indicate that the transcriptomic program typical to mesenchymal stem cells decreased, while the cells gained adipose tissue like properties (panel B vs. C). At the 0 h time point all adipose tissue differentiation related genes are expressed at levels typical to mesenchymal stem cells with no resemblance to adipose tissue. At the 7d time point all these genes have acquired expression level typical to adipose tissues with no resemblance to MSC-style patter matching expression levels. Lipid and fatty acid transport gene set members show a similar tendency.