dSLAM.GPL1444 {SLGI} | R Documentation |
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).
data(dSLAM.GPL1444) data(dSLAM)
dSLAM.GPL1444 is a data frame with 21991 observations on the following 10 variables.
ID
ROW
COLUMN
TAGTYPE
PROBE
ORF
GENE
SEQUENCE
SGDID
SPOT_ID
dSLAM is a character vector of length 5641 that contains the unique and valid systematic ORF names.
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 YEAST data package.
The data were extracted from the Gene Expression Omnibus (GEO) website: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1444
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