Abstract | Cell sizes emerge in the model, which predicts that a single CDK-cyclin pair per growth phase suffices for size control in budding yeast, despite the necessity of the cell cycle network around the cyclins to integrate other cues. |
Introduction | It emerges as a combination of the cell cycle , controlling the orderly orchestration of duplication and division, and the individual growth rate, reflecting extra and intracellular physiological conditions. |
Introduction | The cell cycle and the growth rate are coupled, such that proliferation and growth are balanced, avoiding abnormally large or small cells. |
Introduction | First, the cell cycle as well as cellular growth are two fundamental properties that can be found in nearly all forms of life. |
Applications | In particular we analyze two datasets: the cell cycle dataset in yeast, a common model organism, and a well characterized human leukemia dataset. |
Applications | Yeast T Fs are cooperative during cell cycle . |
Applications | We used Loregic to characterize the TF-TF-target logics during the yeast cell cycle (Materials and Methods) and found 4,126 TF-TF-tar-get triplets that are gate-consistent (Fig. |
Introduction | We apply Loregic to study regulatory factors (TFs and miRNAs) in the yeast cell cycle and human cancer datasets. |
Loregic applications for other regulatory features | We apply Loregic to find the logic operations that characterize the FFLs from a genome-Wide perspective in both the yeast cell cycle and human leukemia cancer datasets. |
Abstract | Transcripts are characterized by decreased halflife: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. |
Discussion | More, we show that ORFs with peak in 3’ UTR share a number of common functions in biological processes such as cell cycle regulation or stress response. |
Discussion | The second one is their enrichment in genes related to cell cycle regulation, apoptosis or similar processes involved in cancer development [65]. |
Discussion | Coherently with the above described functional aspects, flexibility peaks in yeast occur in ORFs involved in cell cycle control or stress response, where flexible sequences seemed to play a regulatory role in gene expression. |
Insights into the functions of ORFs with peak in 3’UTR | The outcomes for Biological Process GO terms (visualized as treemap in supporting 81 file, figure 6, top) point out the presence of ORFs with role in cell cycle , phosphorus/ organic cyclic compound/ nitrogen compound metabolism, phosphorylation reproduction, growth, response to acid, signaling. |
Insights into the functions of ORFs with peak in 3’UTR | The 175 ORFs include genes expressing key components of cell cycle progression and regulation: TUBZ and TUB3 encoding a and fl tubulins, CLB4 and PH 080 encoding cyclins, CDC53 and APC9 encoding respectively the cullin structural protein of SCF complexes and a subunit of the Ana-phase-Promoting Complex/Cyclosome; moreover, AME] , RAD24, RAD59 and SWEI involved in checkpoint maintenance, the F U83, DI G2 and SLT2 encoding MAP-kinases and their regulator BMH1 encoding the major isoform of 14-3-3 proteins. |