Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments Emre Sefer, Michael Kleyman, Ziv Bar-Joseph Cell.

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Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments Emre Sefer, Michael Kleyman, Ziv Bar-Joseph Cell Systems Volume 3, Issue 1, Pages 35-42 (July 2016) DOI: 10.1016/j.cels.2016.06.007 Copyright © 2016 Elsevier Inc. Terms and Conditions

Cell Systems 2016 3, 35-42DOI: (10.1016/j.cels.2016.06.007) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 1 Examples of Piecewise Linear Functions Analyzed in This Work A step function (red) and a more-complex transition function (black). Transition times are denoted by Sgi. Blue, yellow, and green lines at the bottom represent the sampled points by Dense, Repeat2, and Repeat3 strategies, respectively. Cell Systems 2016 3, 35-42DOI: (10.1016/j.cels.2016.06.007) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 2 Comparison of Expected Error for Both Dense and Repeat Strategies (A–C) Comparison of the strategies for different number of experiments and noise levels. (A) Twelve experiments, (B) 24 experiments, and (C) different number of experiments for a fixed noise σ = 0.3 are shown. (D–F) Comparison of sampling strategies for different noise levels over 12 experiments in terms of expected area difference. (D) Fluctuating profile with three transitions is shown. (E) Monotonically increasing profile is shown. (F) Comparison of Dense and Repeat2 and Repeat3 strategies for recovering a profile for which the directions are unknown is shown. The real data are generated from a fluctuating profile with three transitions, though these are not known in advance and so the likelihood function used to select the transition points and directions for both Dense and Repeat does not use this information. Results presented for different noise levels when performing 12 experiments are shown. Cell Systems 2016 3, 35-42DOI: (10.1016/j.cels.2016.06.007) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 3 Comparison of Dense and Repeat Strategies for Genes in Anopheles gambiae (A and B) Comparison of strategies over all genes of Anopheles gambiae by increasing number of experiments over (A) LD data and (B) DD data. (C–E) Comparison of the two strategies on individual genes by eight experiments (C) AGAP010658, (D) AGAP000987, and (E) AGAP001856. The values used for the dense interpolation came from a single data point at times of 12, 20, 28, 32, 40, 48, 56, and 60 hr. The values used for the interpolation of Repeat2 came from both data points at times of 12, 28, 44, and 60 hr. Cell Systems 2016 3, 35-42DOI: (10.1016/j.cels.2016.06.007) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 4 Comparison of Dense and Repeat Strategies for Circadian Genes (A and B) Comparison of strategies over all genes exhibiting circadian and diel rhythms by increasing number of microarrays over (A) LD data and (B) DD data. SD of the error is estimated over the considered genes. (C and D) Comparison of strategies over all genes exhibiting circadian and diel rhythms, where individual genes are sorted by decreasing MSE difference between Dense and Repeat2 when using eight experiments over LD and DD data, respectively. MSE is computed between spline interpolations for each strategy and left out data points. Cell Systems 2016 3, 35-42DOI: (10.1016/j.cels.2016.06.007) Copyright © 2016 Elsevier Inc. Terms and Conditions