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Duygu Varol,Vilda Purutçuoğlu,Remziye Yılmaz 한국유전학회 2018 Genes & Genomics Vol.40 No.2
The aim of this study is to explore the effects of heat stresses on global gene expression profiles and to identify the candidate genes for the heat stress response in commercial baker’s yeast (Saccharomyces cerevisiae) by using microarray technology and comparative statistical data analyses. The data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis, all required statistical methods were performed comparatively. For the normalization step, among alternatives, the RMA (Robust Microarray Analysis) results were used. To determine differentially expressed genes under heat stress treatments, the fold-change and the hypothesis testing approaches were executed under various cut-off values via different multiple testing procedures then the up/down regulated probes were functionally categorized via the PAMSAM clustering. The results of the analysis concluded that the transcriptome changes under the heat shock. Moreover, the temperature-shift stress treatments show that the number of differentially up-regulated genes among the heat shock proteins and transcription factors changed significantly. Finally, the change in temperature is one of the important environmental conditions affecting propagation and industrial application of baker’s yeast. This study statistically analyzes this affect via one-channel microarray data.
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APPLICATION OF IMPULSIVE DETERMINISTIC SIMULATION OF BIOCHEMICAL NETWORKS VIA SIMULATION TOOLS
GOKCE TUNCER,VILDA PURUTCUOGLU 장전수학회 2017 Proceedings of the Jangjeon mathematical society Vol.20 No.1
In order to understand the possible behaviour of biochemi- cal networks, deterministic and stochastic simulation methods have been developed. However in some cases, these methods should be broaden. For example, if the biochemical system is subjected to the unexpected effects causing abrupt changes in the network, the ordinary simulation algorithms cannot capture these impulsive expressions. In this study, we select the simulations tools, specifically, COPASI and Systems Biology Toolbox for MATLAB among alternatives that en- able us to represent the impulsive changes in the system via impulsive or adaptive deterministic simulation algorithms. Accordingly, we com- pare these tools by applying the two major impulsive scenarios, namely, impulses for fixed times and fixed states, based on their accuracies and computational demands. We evaluate our results for small and large systems, respectively.
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