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Computational Analysis of Promoter Elements and Chromatin Features in Yeast

  • John J. WyrickEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 809)

Abstract

Regulatory elements in promoter sequences typically function as binding sites for transcription factor proteins and thus are critical determinants of gene transcription. There is growing evidence that chromatin features, such as histone modifications or nucleosome positions, also have important roles in transcriptional regulation. Recent functional genomics and computational studies have yielded extensive datasets cataloging transcription factor binding sites (TFBS) and chromatin features, such as nucleosome positions, throughout the yeast genome. However, much of this data can be difficult to navigate or analyze efficiently. This chapter describes practical methods for the visualization, data mining, and statistical analysis of yeast promoter elements and chromatin features using two Web-accessible bioinformatics databases: ChromatinDB and Ceres.

Key words

Transcription factor binding sites TFBS Nucleosome positions Histone modifications Data visualization Data mining Statistical analysis Saccharomyces cerevisiae 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.School of Molecular Biosciences and Center for Reproductive BiologyWashington State UniversityPullmanUSA

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