dSLAM.GPL1444: dSLAM platform used for Synthetic Lethal screens in the Boeke Lab

Description

These data are the 21991 probes spotted on the dSLAM array (heterozygote diploid-based synthetic lethality analyzed by microarray) used to test synthetic lethal interactions by Pan et al (2006).

Usage

data(dSLAM.GPL1444)
data(dSLAM)

Arguments

Format

dSLAM.GPL1444 is a data frame with 21991 observations on the following 10 variables.

ID: Serial identifier for probe.
ROW: Row number in the array as scanned with GenePix scanner.
COLUMN: Column number in the array as scanned with GenePix scanner.
TAGTYPE: Code for whether tag is 5' (Up) or 3' (Dn) relative to the open reading frame (ORF).
PROBE: Code for singleton probes arrayed in ORF order (ArrA, ArrB), five-fold replicate probes arrayed in randomized order (Rpts), systematic mutations arrayed across the center of the array (Muts), negative controls (NegT), or probes peripheral to the array as specified by the manufacturer (Edge)
ORF: Systematic ORF name (from SGD, Feb 2003) (http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=
GENE: Standard gene name (SGD) (or ORF if not available)
SEQUENCE: DNA sequence of probe (includes custom-designed sequences for 193 YA* and YM* ORFs missing DnTags)
SGDID: Unique ORF identifier from SGD; 'S000000000' denotes missing value
SPOT_ID: spot identifier; ('YQL' ORFs denote custom-designed sequences; 'NegA', 'NegB', 'PosA', 'PosB' denote proprietary sequences specified by the manufacturer)

dSLAM is a character vector of length 5641 that contains the unique and valid systematic ORF names.

Source

The data were extracted from the Gene Expression Omnibus (GEO) website: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1444

Details

The dSLAM.GPL1444 were directly obtain from parsing the GPL1444\_family.soft.gz available at http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1444

dSLAM is a vector of length 5641, extracted from the dSLAM.GPL1444 ORF, and that contains the unique and valid systematic ORF names. This vector was built in three steps. First the ORFs with SGDID equals to S000000000 in the dSLAM.GPL1444 data frame were removed as some correspond to custom sequences and other were dubious ORFs that have been deleted from SGD or merged with other ORFs. Secondly, the duplicated names were removed. Then, the systematic ORF names were verified against the org.Sc.sgd.db data package.

References

Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 2006 Mar 10;124(5):1069-81