Additional file 2.

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This file contains an animation demonstrating the effect of varying the FIR score threshold for including genes in the SCGS. For each possible number of top-scoring stem genes from 3-502 (displayed at the top of the animation frame), we project all of the samples in the database into the first two PCs of gene space (panel on top right), and highlight in color six relevant phenotypes (as in Figure 3): embryonic/induced pluripotent stem cells in magenta; mesenchymal stem cells in cyan; immortalized cell line samples in blue; blood precursor cells in orange; leukemia samples in green; normal blood in red. The panel below the PCA scatter plot shows the distribution of stemness index values (PC1 projection coordinates) for each highlighted phenotype. The plot on the left of the frame shows the analysis of variance (ANOVA) score (including all highlighted phenotypes) for the clustering defined by the current stemness index highlighted by a magenta dot on the curve showing all ANOVA scores for all of the depicted FIR thresholds. Higher ANOVA scores indicate better multi-way separation of the individual phenotypes along the stemness index. ANOVA was calculated and all plots were generated in the R statistical environment [46,47].

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Palmer et al. Genome Biology 2012 13:R71   doi:10.1186/gb-2012-13-8-r71