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Distribution Maps of Rap1p and Sir Proteins  
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Supplement 
Figures and analysis not included in the paper
Important note: The links in this section are to GIF and PDF files. If you click the link, the file will open in your web browser. To save the file to your computer, please use the "Save link as..." or "Save target as..." feature of your browser. Windows users right-click the link, and Mac users control-click or click-and-hold the link. Adobe Acrobat Reader 3.0 or later is required. If you need the Adobe Acrobat Reader, click here. See also the References and Disclaimer for the supplemental data.

Annotated Pathways

Download or View Web Figure F, PDF (or higher-resolution GIF), an annotated glycolysis pathway showing Rap1p's role in regulating glycolysis.

Rap1p targets form a continuous enzymatic pathway in glycolysis from fructose-1,6-biphosphate to ethanol. Genes in red are Rap1p targets. Genes in green are not Rap1p targets. An asterisk (*) marks previously known targets, and (hc) marks spots that had a high rank in both IP and control experiments. This map was based on the glycolysis pathway provided by the Kyoto Encyclopedia of Genes and Genomes (KEGG).
 

Rap1p Motif Finding

BioProspector - Find out more about the program, and submit your own sequences for analysis

Download Web Table E, motif matrices for Rap1p binding sequence, as determined by BioProspector's analysis of Rap1p IP'd fragments.

 

Relationships between Expression Data and Rap1p IP data

Note: RPG = Ribosomal Protein Gene

Web Figure H, the .cdt and .gtr files corresponding to the cluster of gene expression profiles for the genes downstream of intergenic fragments selected by the Rap1p IP. Treeview is required to view the clusters.

    Please note the the clusters were created using more experiments than are shown. Only published experiments, or experiments for which researchers agreed to have thier data released in this form are shown.

Download or View Web Figure I, a graph of the relationship between an ORF's correlation to the average RPG expression profile and the position of any upstream occurrence(s) of the Rap1p consensus binding site.

Rap1p binding sites tend to occur from 225 to 400 base pairs upstream of genes that are regulated like RPGs. The graph was created by finding all occurrences of the degenerate sequence MAYCCRNNCA that occur within 1000 base pairs of the start codon of any ORF, and sorting based on the position of each hit. A moving average of each ORF's correlation to the ribosomal protein gene expression pattern was then calculated, with a window size of 40.
 

Download or View Web Figure J, a graph of the relationship between an ORF's correlation to the average RPG expression profile and the relative strandedness of upstream Rap1p binding sites.

Rap1p binding sites tend to occur on the (-) strand relative to genes that are regulated like RPGs. The graph was created by sorting according to each ORF's correlation to the ribosomal protein gene expression pattern, then taking a moving average of the strandedness of any MAYCCRNNCA hits that were recorded within 1000 base pairs of the start codon. A value of 1 was assigned to each hit recorded on the + strand (the same strand as the coding sequence) and a score of -1 was assigned to each hit recorded on the - strand (the strand opposite the coding sequence). Only ORFs with an upstream MAYCCRNNCA hit are included in this plot.

Download or View a graph of the relationship between an ORF's correlation to the average RPG expression profile and its promoter's Rap1p IP percentile rank.

The promoters of genes regulated like RPGs are enriched in Rap1p IPs. The graph was created by sorting according to each ORF's correlation to the ribosomal protein gene expression pattern, then taking a moving average of its promoter's IP percentile rank, with a window size of 40.

Download or View a graph of the relationship between an ORF's correlation to the average RPG expression profile and its promoter's motif score.

The promoters of genes regulated like RPGs tend to have higher Rap1p DNA binding motif scores. The graph was created by sorting according to each ORF's correlation to the ribosomal protein gene expression pattern, then taking a moving median of its promoter's motif score, with a window size of 20.

Download or View a graph of the relationship between an ORF's transcript abundance and its promoter's Rap1p IP percentile rank (RPGs Excluded).

The promoters of genes with very high expression levels and very low expression levels are enriched in Rap1p IPs. The tail to the left represents telomeric ORFs, and the tail to the right represents internal targets. The peak to the right would be more pronounced if RPGs were included in the analysis.The graph was created by sorting according to the copy number percentile rank, then taking a moving average of its promoter's motif score, with a window size of 40.

Other Data Analysis

Download or View WEB FIGURE D, showing the extent of each protein's association with each chromosome end (keeping in mind the caveats discussed in the text).

Download or View WEB FIGURE G, graphs showing the functional classifications of Rap1p targets compared to functional classification of all yeast ORFs.

Download or View a graph of the relationship between an ORF's correlation to the average RPG expression profile and its transcript abundance.

This graph does not contain any IP data, but is an interesting observation. Across the entire yeast genome, for every class of yeast gene, as genes become more highly expressed, their regulation across diverse environmental conditions more closely resembles that of the ribosomal protein genes. The graph was created by sorting according to the copy number percentile rank, then taking a moving average of each ORF's correlation to the ribosomal protein gene expression pattern with a window size of 40.

Download or View a histogram of the mean percentile rank distributions for the Sir protein IP experiments.

 

 

 

 


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