This web page is a supplement
to:
Christopher Wade, Kathleen Shea,
Roderick Jensen, and Michael A. McAlear. EBP2 Is a Member
of the RRB Regulon, a Transcriptionaly Co-regulated Set of Genes That Are
Required for Ribosome and rRNA Biosynthesis. MCB, Dec 10, Vol.21,
No.24. pXX-XX.
1) The alpha factor clusters:
Description
To download an Excel file detailing the membership of 24 clusters in the alpha factor experiment, click here.
2) The sporulation clusters:
Description
To download an Excel file detailing the membership of 24 clusters in the sporulation experiment, click here.
3) Promoter search using Motif1 and 2 MEME consensus sequences on the entire yeast genome
In order to identify the set of yeast genes that contain Motif I and Motif II sequences within their promoters, we did an alignment search covering yeast genome. This search was done using the MAST (Motif Alignment and Search Tool) program version 3.0. The MAST program looked at -950bp to 50bp of each yeast ORF (as opposed to the 500bp upstream used for our MEME search) using the same sequence with corresponding degeneracy used for generating our MEME motifs reported in the paper. Using a cutoff value of E<20, the MEME program identified 317 ORF's that contain promoter sequences similar to the motifs associated with the RRB cluster. Since the promoter regions of two genes can overlap, both would be identified even though the motifs may be functionally linked to only one. The attached file includes the MAST readout. The first section lists the 317 genes with their corresponding E values, the second section shows their location and orientation, and the third shows the actual sequence alignments. For further information please see http://meme.sdsc.edu or Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(48-54), 1998.
To view the results of this search in your web-browser, click here.
To download the results, click the link above and then use the save option in your web-browser.
For further information, please
contact Dr. Michael McAlear at mmcalear@wesleyan.edu