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Distribution Maps of Rap1p and Sir Proteins  
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A Detailed Description of the Methods Used  
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Welcome to the web supplement for "Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association". Here you can find electronic versions of the paper and figures, in addition to data and detailed analysis not included in the print version. Follow this link to the paper on the Nature Genetics site.

IMPORTANT NOTICE 01-16-02: The Motif Score values listed in previous versions of Web Table A were incorrect. This table has been updated. Other tables report the correct motif scores, and were not affected.

The Paper section contains links to all of the Web Figures and Tables that are mentioned in the text, as well as electronic versions of the paper and figures as they were printed.

The Stanford Microarray Database hosts links to images of each array used in the paper, clickable array images, downloadable raw data, and experimental details linked to each array.

Click the icon to browse, analyze, or download the data from within the Stanford Microarray Database
Lieb et al. IP data from SMD

Alternate instructions: From the home page, choose "Public Search" and then "Basic Search". On the Basic Search page, in Part I choose "Publications" and in part II choose "Saccharomyces cerevisiae" and "Lieb et al.". Finally, click the "Display Data" button to view individual experiments, or the "Data Retrieval and Analysis" button to filter, cluster, analyze, and download the data.

The Maps section contains annotated maps of the distribution of Rap1p, Sir2p, Sir3p, and Sir4p. The maps in this section differ slightly from Figure 2. They retain "lankmark" labels along the chromosome.

The Download area contains the tabular numerical data from all of the experiments. This is where to find the raw ratio and percentile data for every arrayed segment, a list of all ORFs affected by sites of Rap1p and Sir protein association, all of the data used to make the graphs in Paper and Supplement sections, and a variety of other statistics and lists. The files in this section are in tab-delimited text format, which can be imported easily into any spreadsheet application.

The Supplement section contains the supplemental figures that are referred to in the text, and additional graphical representations of the numerical data in the Download section. These include the percentile rank distributions of all fragments for each IP, interesting relationships between gene expression data and IP data, an annotated glycolysis pathway, and "Eisengrams" of the expression levels of ORFs downstream of Rap1p binding sites.

The Methods section provides a detailed description of the protocols and materials used in these experiments.

If you need help, more information, or files in different formats, consult the Contacts page and get in touch.

Be sure to visit the Brown Lab home page.

Many of the files on this site are in PDF format and require Adobe Acrobat Reader 3.0 or later. The reader is available for free from Adobe.


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