Sort PSAMs

Since we are currently interested in PSAMs relevant to a biological process and not a particular PSAM, we continue on and click on the "Sort PSAMs" tab. Here, we are presented with a list of all parsable gene expression "samples" available in GEO for S. cerevisiae. The samples are listed in order of their GEO sample IDs and are labeled with their GEO sample titles. We can view the sample information in GEO by clicking on the "GEO" link across from the sample title. We know the GEO IDs of the samples we are interested in from our previous browsing of GEO. Thus, we scroll down the page to GEO IDs GSM87588 to GSM87623, which cover the series of experiments that follow a shift from sporulation to rich media at various sporulation time points, in addition to a reference sporulation time course. We click on the links for each of these samples in turn. Each link presents us with a list of PSAMs sorted by the goodness of fit (absolute t-value) of their predicted promoter occupancy [3] to the expression values in the experiment of interest (example). Also shown are P-values corresponding to the t-values and E-values, which are P-values corrected for the number of PSAMs that have been sorted. We write down a selection of highly significant PSAMs (E-value <= 10^-3) for multiple sporulation samples. Where there are multiple PSAMs for a particular TF, we choose one high-scoring representative. We now have a list of PSAMs for TFs that may be involved in the transcriptional regulation of sporulation.