Meta-transcriptome Analysis

Medians and 25%/75% quantiles of the log2 fold changes (over means) of YRO cohorts in various experiment series.

Growth Rate Gradients

Data by Slavov and Botstein (2011), Brauer et al. (2008), Xia et al. (2022), Paulo et al. (2016), Hackett et al. (2016), Jackson et al. (2020).

Stress Conditions

Cyclin Mutants

Data by Orlando et al. (2008), Bristow et al. (2014), Cho et al. (2017), Simmons Kovacs et al. (2012), Campbell et al. (2020).

References

Brauer, M. J., C. Huttenhower, E. M. Airoldi, R. Rosenstein, J. C. Matese, D. Gresham, V. M. Boer, O. G. Troyanskaya, and D. Botstein. 2008. "Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast." Mol Biol Cell 19 (1): 352-67. https://doi.org/10.1091/mbc.E07-08-0779.

Bristow, S. L., A. R. Leman, L. A. Simmons Kovacs, A. Deckard, J. Harer, and S. B. Haase. 2014. "Checkpoints Couple Transcription Network Oscillator Dynamics to Cell-Cycle Progression." Genome Biol 15 (9): 446. https://doi.org/10.1186/s13059-014-0446-7.

Campbell, K., J. Westholm, S. Kasvandik, F. Di Bartolomeo, M. Mormino, and J. Nielsen. 2020. "Building Blocks Are Synthesized on Demand During the Yeast Cell Cycle." Proc Natl Acad Sci U S A 117 (14): 7575-83. https://doi.org/10.1073/pnas.1919535117.

Cho, C. Y., F. C. Motta, C. M. Kelliher, A. Deckard, and S. B. Haase. 2017. "Reconciling Conflicting Models for Global Control of Cell-Cycle Transcription." Cell Cycle 16 (20): 1965-78. https://doi.org/10.1080/15384101.2017.1367073.

Gasch, A. P., F. B. Yu, J. Hose, L. E. Escalante, M. Place, R. Bacher, J. Kanbar, et al. 2017. "Single-Cell RNA Sequencing Reveals Intrinsic and Extrinsic Regulatory Heterogeneity in Yeast Responding to Stress." PLoS Biol 15 (12): e2004050. https://doi.org/10.1371/journal.pbio.2004050.

Hackett, S. R., V. R. Zanotelli, W. Xu, J. Goya, J. O. Park, D. H. Perlman, P. A. Gibney, D. Botstein, J. D. Storey, and J. D. Rabinowitz. 2016. "Systems-Level Analysis of Mechanisms Regulating Yeast Metabolic Flux." Science 354 (6311). https://doi.org/10.1126/science.aaf2786.

Jackson, C. A., D. M. Castro, G. A. Saldi, R. Bonneau, and D. Gresham. 2020. "Gene Regulatory Network Reconstruction Using Single-Cell RNA Sequencing of Barcoded Genotypes in Diverse Environments." Elife 9 (January). https://doi.org/10.7554/eLife.51254.

Orlando, D. A., C. Y. Lin, A. Bernard, J. Y. Wang, J. E. Socolar, E. S. Iversen, A. J. Hartemink, and S. B. Haase. 2008. "Global Control of Cell-Cycle Transcription by Coupled CDK and Network Oscillators." Nature 453 (7197): 944-47. https://doi.org/10.1038/nature06955.

Paulo, J. A., J. D. O'Connell, R. A. Everley, J. O'Brien, M. A. Gygi, and S. P. Gygi. 2016. "Quantitative Mass Spectrometry-Based Multiplexing Compares the Abundance of 5000 s. Cerevisiae Proteins Across 10 Carbon Sources." J Proteomics 148 (October): 85-93. https://doi.org/10.1016/j.jprot.2016.07.005.

Simmons Kovacs, L. A., M. B. Mayhew, D. A. Orlando, Y. Jin, Q. Li, C. Huang, S. I. Reed, S. Mukherjee, and S. B. Haase. 2012. "Cyclin-Dependent Kinases Are Regulators and Effectors of Oscillations Driven by a Transcription Factor Network." Mol Cell 45 (5): 669-79. https://doi.org/10.1016/j.molcel.2011.12.033.

Slavov, N., and D. Botstein. 2011. "Coupling Among Growth Rate Response, Metabolic Cycle, and Cell Division Cycle in Yeast." Mol Biol Cell 22 (12): 1997-2009. https://doi.org/10.1091/mbc.E11-02-0132.

Xia, J., B. J. Sanchez, Y. Chen, K. Campbell, S. Kasvandik, and J. Nielsen. 2022. "Proteome Allocations Change Linearly with the Specific Growth Rate of Saccharomyces Cerevisiae Under Glucose Limitation." Nat Commun 13 (1): 2819. https://doi.org/10.1038/s41467-022-30513-2.