Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis
Transcriptional regulation is one of the key steps in the control of gene expression, with huge impact on the survival, adaptation, and fitness of all organisms. However, it is becoming increasingly clear that transcriptional regulation is far more complex than initially foreseen. In model organisms such as the yeast Saccharomyces cerevisiae evidence has been piling up showing that the expression of each gene can be controlled by several transcription factors, in the close dependency of the environmental conditions. Furthermore, transcription factors work in intricate networks, being themselves regulated at the transcriptional, post-transcriptional, and post-translational levels, working in cooperation or antagonism in the promoters of their target genes.
In this chapter, a step-by-step guide using the YEASTRACT database is provided, for the prediction and ranking of the transcription factors required for the regulation of the expression a single gene and of a genome-wide response. These analyses are illustrated with the regulation of the PDR18 gene and of the transcriptome-wide changes induced upon exposure to the herbicide 2,4-Dichlorophenoxyacetic acid (2,4-D), respectively. The newest potentialities of this information system are explored, and the various results obtained in the dependency of the querying criteria are discussed in terms of the knowledge gathered on the biological responses considered as case studies.
Key wordsYEASTRACT Transcriptional regulation prediction Transcription regulatory networks Transcriptomic data analysis Saccharomyces cerevisiae
Deep recognition is extended to all present and former YEASTRACT team members that over the years have contributed to the retrieval and curation of transcriptional regulatory data (Sandra Tenreiro, Nuno P Mira, Alexandra R Fernandes, Artur Lourenço, Sandra C dos Santos, Tânia R Cabrito, Catarina Costa, Joana Guerreiro, Margarida Palma, Marta Alenquer) and to the generation of computational tools (Ana T Freitas, Arlindo L Oliveira, Nuno Mendes, Dário Abdulrehman, Pooja Jain, Alexandre P Francisco, Sara C Madeira, Alexandra M Carvalho, Hélio Pais, Joana P Gonçalves, Ricardo S Aires, Sofia D’Orey) that make YEASTRACT such a powerful database. We are also grateful to colleagues and friends from the international Yeast and Systems Biology Communities for their encouragement and suggestions. Funding for the development and maintenance of the YEASTRACT database was partially and indirectly obtained from Fundação para a Ciência e a Tecnologia (FCT) through PhD and postdoctoral scholarships to the members of the YEASTRACT teams. Funding received by iBB-Institute for Bioengineering and Biosciences(UID/BIO/04565/2013) from the Portuguese Foundation for Science and Technology (FCT) is acknolwedged.
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