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Figure 2 | BMC Genomics

Figure 2

From: Pathway reporter genes define molecular phenotypes of human cells

Figure 2

Molecular phenotyping of iPSC-derived cardiomyocyte differentiation. (A) Principal component analysis using microarray data of ~22,000 genes (top) and AmpliSeq-RNA data of 917 pathway reporter genes (bottom). (B) Pathway activity scores based on expression of pathway reporter genes reported by the GSVA algorithm: pathways are sorted by the time when its activity score reaches the maximum. GSVA scores were calculated for each sample and the average values of each pathway at each time point are reported. To allow between-pathway comparisons, the scores are normalized by row using the z-score transformation (zero mean and unit variance). Pathway names can be found in Additional file 3. (C) Activity patterns of selected pathways. Two representatives are chosen from stem-cell specific, ‘switch’, and cardiomyocyte-specific pathways, respectively. (D) Expression of key reporter genes of the Hedgehog pathway. (E) Expression of selected functional markers of pathways associated with differentiated cardiomyocytes. For comparison, subfigure c, d, and e also include the activity scores and expression profiles reported by microarray.

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