Supplementary Materials Supporting Information pnas_0604860103_index. mapped right into a basic 3D figure. As opposed to transcripts in the late-reductive stage, most transcripts usually do not display transients Dexamethasone inhibitor in expression in accordance with others within Rabbit polyclonal to KBTBD8 their temporal cluster but modification their period in a concerted style. Mapping the trajectories of the transcripts into low-dimensional areas which can be represented by basic systems of differential equations offers a easily testable style of the powerful architecture of phenotype. In this technique, period doubling could be a desired pathway for phenotypic change. As a practical matter, low-amplitude, genome-wide oscillations, a ubiquitous but often unrecognized attribute of phenotype, could be a source of seemingly intractable biological noise in microarray studies. and 8, which is published as supporting information on the PNAS web site). Similarly, in the early-reductive phase, oscillations in transcripts do not show the same genome-scale changes until after the expansion of the late-reductive period, as can be seen in Fig. 1 and in the expanded map of the late-reductive phase transcripts in Fig. 2and Dexamethasone inhibitor early and respiratory phase transcripts (Fig. 2 and axis in and represents time in minutes. As in Fig. 1, intensity was scaled Dexamethasone inhibitor from 0.2 (dark blue) to 4 (red-orange). In as a 3D projection that emphasizes the globally cyclic nature of expression. The expansion of the trajectory in the third cycle and the increase in the number of maxima in expression seen in and and captured principally by Eigengenes 3 and 4 are seen in the Figs. 13 and 14. For comparison, a 3D reconstruction of the trajectory of transcript concentration from the averages of the scaled data of three major temporal clusters from Fig. 2above is shown. The projection emphasizes the globally cyclic nature of the system. For comparison, a more transparent method was used. The average of the three major temporal clusters of Figs. 1 and ?and22 are shown in Fig. 2and plotted together in Fig. 3as a 3D reconstruction of the trajectories through concentration phase space of the four cycles of the experiment (Fig. 3component of the attractor drawn here (red line in Fig. 5and variables of the R?ssler. Open in a separate window Fig. 5. Mapping period doubling onto a low-dimensional surface. A sketch of proposed paths in concentration phase space of the transcripts is shown based on the R?ssler attractor. (and indicate the path that would be followed by late-reductive transcripts to reach the levels seen in the first cycle Dexamethasone inhibitor after treatment cycle 2. (and and 14, which is published as supporting information on the PNAS web site). It seems the SVD analysis captures this response in the third and forth cycles after treatment (Fig. 3 and Genome Database (SGD) site, and both their genetic and physical map locations were associated with the intensity values for each gene as described (4). The results for all ORFs scored as present by using the default Affymetrix settings were identified according to the original sample number and the phase in the DO oscillation at which the maximum expression occurred. Expression patterns were then mapped according to the time of maximum as a starting point for presentation. Further analysis was performed for all ORFs present in all samples in each of the four cycles. Of the 5,443 ORFs scored as present in at least 3 of the 48 samples, 5,254 had values 0.01 and the remainder had values 0.035 (detailed methods and sample calculations are available in em Supporting Methods /em ). Original data are available from the National Center for Biotechnology Information/Gene Expression Omnibus web site. Supplementary Material Supporting Information: Dexamethasone inhibitor Click here to view. Acknowledgments We thank Paul Frankel of the Biostatistics Department for help in translating the R?ssler attractor, Maricela Covarrubias of the Functional Genomics core facility for help with sample preparation and analysis, Ariel Klevecz of the Dynamics Group for help with informatics and early experiments with PZ and monoamine oxidase homologues, and Tim Synold and the Mass Spectrometry Core Facility for analysis of PZ levels in cells and medium. Abbreviations PZphenelzineSVDsingular value decompositionDOdissolved oxygenTRACtranscriptional-respiratory-attractor cycle. Footnotes The authors declare no conflict of interest. This article is a PNAS immediate submission. Discover Commentary on page 16063..