Fig. 2

The Daphnia genome is expressed in a highly rhythmic manner. a Hierarchical clustering of rhythmic Daphnia genes. Yellow indicates higher expression, and blue indicates lower expression versus the mean value for each gene. All 1,661 Daphnia genes identified as rhythmic by JTK_CYCLE are displayed. The heat map on the right is a continuation of the one on the left. b Example gene expression profiles of select genes with low JTK_CYCLE q-values. Note the diversity in time-of-peak expression (phase), amplitude of rhythms, and raw-intensity values. Error bars represent S.E.M. of technical replicates. For two of these genes, we performed qRT-PCR confirmation, see Additional file 3. c Histograms of rhythmic gene amplitude (peak-to-trough fold change) and times of peak expression. The 1,661 genes called rhythmic by JTK_CYCLE had a median fold change of 2.06. However, there are a significant number of rhythmic genes with a greater than 5-fold amplitude in expression. Peaks of transcriptional expression occur at mid-day and mid-night. Day and night are indicated by the horizontal white/black bars. Histogram X-axis values reflect the minimum fold change/time-of-day reflected in that bin (i.e. >1, ≥1.5, ≥2.0, ≥2.5, etc)