Temporal profiling and network analysis of rhythmic gene expression and novel functional gene annotation in the water flea, Daphnia pulex

We analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 48 hr time period using a cosine-fitting algorithm. Additionally, using a comprehensive network modeling and analysis approach, we go beyond the standard statistical analyses of the gene expression data. By doing so, we identified novel co-regulated rhythmic genes that have similar network topological as well as functional annotations as rhythmic genes identified by the statistical analyses but that cannot be identified by cosine-fitting alone. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus complementing the current limited functional annotation data. Our results revealed extensive 24 hr rhythms in gene expression patterns. Moderate longitudinal study of circadian rhythm with twelve 4-hour period measurements collected over the course of 48 hours. See Supplimental Image - Modified Loop Design.png Periodic measures were compared in a nearly saturated modified loop design with N-period time point compared with N+4-hour period time point, followed by N-period time point compared with N+12-hour period time point. The loop is closed with N+4-hour period time point compared with N-period time point and N+12-hour period time point compared with N-period time up to the 3rd cycle.