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    The numerical data used in the paper and more
Important note: Most of the links in this section are to Tab-delimited text 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. See also the References and Disclaimer for this page.

General

Download the genomic position of every arrayed fragment. The reported positions are from the SGD coodinates as of May 1999, so there may be discrepancies between the values reported here and current coordinates, particularly on chromosome III.

Download WEB TABLE D, a list of all ORFs and their corresponding "gene-ness"score. ORFs with a score below 0 were considered "questionable".

Each ORF has been given a single score that reflects the likelihood of it being a gene, based on the following criteria:

Codon Usage
MIPS Class
Overlap with another ORF
SAGE Tag
YPD description
Amino Acid Length
Gene Expression Data

Each criterion was subjectively weighted, and is listed above from heaviest to lightest weight. Among ORFs with a score <0, there are 10 named genes (1.1%). 1 is an RNA gene, 1 is known to be non-coding, 7 have no references or functions associated with them, and only 1 has strong similarity to a known gene. Using the 0 cutoff, 874 ORFs are classified as "questionable".

Rap1p and Sir Protein Data

Download tables containing the distribution of percentile ranks for the Rap1p and Sir protein IPs.

Download details about the extent of Rap1p and Sir protein binding at chromosome ends.

Download the superset of all spotted segments selected in Rap1p or Sir protein IPs.

 

Rap1p Data
Note: RPG = Ribosomal Protein Gene

Download the raw percentile rank data for every spotted segment, for each control and Rap1p IP.

Download WEB TABLE A, the tabular data for the spotted segments that made the cutoff for significance for Rap1p IPs.

Download WEB TABLE B, the tabular data for non-RPG ORFs whose upstream regions are bound by Rap1p.

Download WEB TABLE C, all RPGs and whether Rap1p is bound to their promoters, ORFs, or 3'UTRs.

Download the data used to compare the transcript level that results from each ORF to the Rap1p IP percentile rank of each ORF's promoter.

Download the data used to compare the transcription rate at each ORF to the Rap1p IP percentile rank of each ORF's promoter.

Download information about ORFs that share a promoter with RPGs.

Download statistics about the distribution of Rap1p foci.

Download statistics about the segments selected in Rap1p IPs. (NOTE: this file is in Microsoft Excel Format.)

Download the list of previously known Rap1p targets, used for demonstration purposes in the paper. Only targets with molecular or biochemical confirmation are listed, and this list may not be complete. In finding "known" targets for Rap1p, I searched the literature, but also relied heavily on database sites, including YPD, to gather information. Therefore, some Rap1p targets that had been previously identified may have been missed.

Rap1p Motif Scores

Download the motif score and Rap1p IP percentile rank of all spotted fragments.

Download the Rap1p IP percentile rank and Motif score for the promoter of each ORF.

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

 

Sir Protein Data

Download the raw percentile rank data for every spotted segment, for Sir2p, Sir3p, Sir4p, and control IPs.

Sir2p

Download a list of all segments enriched in Sir2p IPs.

Download a list of the non-telomeric, non-crosshybridizing, low-control segments enriched in Sir2p IPs.

Download WEB TABLE G, a list of the non-telomeric, non-mating type ORFs affected by the distribution of Sir2p.

Sir3p

Download a list of the segments enriched in Sir3p IPs.

Download a list of the non-telomeric, non-crosshybridizing, low-control segments enriched in Sir3p IPs.

Download WEB TABLE H, a list of the non-telomeric, non-mating type loci ORFs affected by the distribution of Sir3p.

Sir4p

Download a list of the segments enriched in Sir4p IPs.

Download a list of the non-telomeric, non-crosshybridizing, low-control segments enriched in Sir4p IPs.

Download WEB TABLE I, a list of the non-telomeric, non-mating type loci ORFs affected by the distribution of Sir3p.

References

The mRNA half-life, mRNA abundance, and transcription rate of ORFs listed in the sheets above was derived from:

Dissecting the Regulatory Circuitry of a Eukaryotic Genome. Holstege, et al.Cell 95:717-728 (1998), and its supplement.

The data concerning transcript levels in rap1 and sir mutants was derived from:

Chromosomal Landscape of Nucleosome-dependent Gene Expression and Silencing in Yeast. Wyrick, et al., Nature 402:418-421 (1999), and its supplement.

Disclaimer

Every attempt has been made to keep these files consistent with each other and up-to-date. However, there are bound to be some small discrepancies between data sheets. These discrepancies arise when new criteria or updated informatics are applied to certain lists but not others. In finding "known" targets for Rap1p, I searched the literature, but also relied heavily on database sites, including YPD, to gather information. Therefore, some Rap1p targets that had been previously identified may have been missed.


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