Figure 7

Change in the expression levels of all genes between time points 8 and 12 in trajectory 1-5-7-8-10-12. Change in the expression levels of all genes between time points 8 and 12 in trajectory 1-5-7-8-10-12 due to the third transcription pattern, ordered by their increasing values. Computed as the α = 3 term in equation (2). Note that while many gene levels do not change, some go up in level while others are reduced. As seen in equation (2), the direction of the change is determined by two factors: a pattern-wide factor that is the difference in the weight of the pattern between the two time points and the (time independent) sign of the weight G _iα of gene i in pattern α. Also shown in the figure, red and brown, are the contributions of the other transcription patterns. These are the terms of other values of α in equation (2). These are, in comparison, smaller since the main transcription pattern that contributes to the change in expression level between point 8 and point 12 is transcription pattern 3. Transcription pattern 3 is most contributory to this change because while overall the transcription patterns 1 and 2 are more heavily weighted, they do not change between point 8 and 12. See Figure 3 and the Additional file 1 Figures S2, S3, S4 and S5.