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The Functional Consequences of Variation in Transcription Factor Binding

Figure 1

Differential expression analysis.

(a) Examples of differential expression analysis results for the genes HCST and IRF4. The top two panels are ‘MA plots’ of the mean Log2(expression level) between the knockdown arrays and the controls for each gene (x-axis) to the Log2(Fold-Change) between the knockdowns and controls (y-axis). Differentially expressed genes at an FDR of 5% are plotted in yellow (points 50% larger). The gene targeted by the siRNA is highlighted in red. The bottom two panels are ‘volcano plots’ of the Log2(Fold-Change) between the knockdowns and controls (x-axis) to the P-value for differential expression (y-axis). The dashed line marks the 5% FDR threshold. Differentially expressed genes at an FDR of 5% are plotted in yellow (points 50% larger). The red dot marks the gene targeted by the siRNA. (b) Barplot of number of differentially expressed genes in each knockdown experiment. (c) Comparison of the knockdown level measured by qPCR (RNA sample collected 48 hours post-transfection) and the knockdown level measured by microarray. (d) Comparison of the level of knockdown of the transcription factor at 48 hrs (evaluated by qPCR; x-axis) and the number of genes differentially expressed in the knockdown experiment (y-axis). (e) Comparison of the variance in knockdown efficiency between replicates for each transcription factor (evaluated by qPCR; x-axis) and the number of differentially expressed genes in the knockdown experiment (y-axis).

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1004226.g001