Below, I show enrichment profiles with other yeast gene
classifications, specifically the SGD's GO annotation, a classification
of yeast genes into their pre-eukaryotic ancestry (Bogumil et al. 2014), and a
classification of cell division cycle phase-specific expression (Spellman et al. 1998)
(numbers are overlap counts, gray-scale indicates p-values from
cumulative hypergeomtric distribution tests, where black is the minimal
shown \(p\le10^{-10}\)), boxplots of
the transcripts tRNA and adaptation indices (Man and Pilpel 2007), and t-test profiles
of the proteins' amino acid compositions (numbers: t statistic; red:
higher, blue: lower than average; color intensity indicates the p-values
with full colors \(p\le10^{-10}\)).
Bogumil, D., D. Alvarez-Ponce, G. Landan, J. O. McInerney, and T. Dagan.
2014.
"Integration of Two Ancestral Chaperone Systems into One:
The Evolution of Eukaryotic Molecular Chaperones in Light of
Eukaryogenesis." Mol Biol Evol 31 (2): 410-18.
https://doi.org/10.1093/molbev/mst212.
Li, C. M., and R. R. Klevecz. 2006.
"A Rapid Genome-Scale Response
of the Transcriptional Oscillator to Perturbation Reveals a
Period-Doubling Path to Phenotypic Change." Proc Natl Acad
Sci U S A 103 (44): 16254-59.
https://doi.org/10.1073/pnas.0604860103.
Machné, R., and D. B. Murray. 2012.
"The Yin and Yang of Yeast
Transcription: Elements of a Global Feedback System Between Metabolism
and Chromatin." PLoS One 7 (6): e37906.
https://doi.org/10.1371/journal.pone.0037906.
Man, O., and Y. Pilpel. 2007.
"Differential Translation Efficiency
of Orthologous Genes Is Involved in Phenotypic Divergence of Yeast
Species." Nat Genet 39 (3): 415-21.
https://doi.org/10.1038/ng1967.
Spellman, P. T., G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B.
Eisen, P. O. Brown, D. Botstein, and B. Futcher. 1998.
"Comprehensive
Identification of Cell Cycle-Regulated Genes of the Yeast
Saccharomyces Cerevisiae by Microarray
Hybridization." Mol Biol Cell 9 (12): 3273-97.
Tu, B. P., A. Kudlicki, M. Rowicka, and S. L. McKnight. 2005.
"Logic of the Yeast
Metabolic Cycle: Temporal Compartmentalization of Cellular
Processes." Science 310 (5751): 1152-58.
