Introduction

We will step through an example of an inquiry using the Yeast Transfactome Database. In the process, we will demonstrate the features of the web interface, extend advice on interpreting results, and generate testable hypotheses for future study.

When using the Yeast Transfactome Database, the user will likely start with a physiological condition or trans-factor of interest. As an example, we choose the transcriptional regulation of sporulation. Browsing the NCBI Gene Expression Omnibus [1], we find a series of experiments in which the authors created microarray time courses for the sporulation of yeast cells [2] . They also performed microarray experiments that measured the changes in yeast gene expression as the researchers replaced sporulation media with rich media at various points during the progression of sporulation. The authors were interested in the gene expression determinants of the commitment to finish sporulation rather than resume mitosis upon transfer to rich media. Using the Yeast Transfactome Database, we can interrogate the contribution to transcriptional regulation of this process by any trans-factor in the database.

We begin at the Yeast Transfactome homepage. Here we may choose between examining DNA-binding proteins or RNA-binding proteins. Currently, genome-wide occupancy data is only publicly available for the five members of the Puf family of RNA-binding proteins in yeast, so the DNA-binding protein section of the database is more substantial, covering hundreds of yeast transcription factors. Since we are interested in the transcriptional program of sporulation, we click on the DNA-binding protein link.