Boeke: Incidence matrix of Synthetic Lethal interaction from the Boeke Lab

Description

Data from Pan et al. experiments on DNA integrity Network in the Yeast S. cerevisiae.

Usage

data(Boeke2006raw)
data(Boeke2006)

Arguments

Format

Boeke2006raw is a data frame with 5775 observations on the following 6 variables.

Query.ORF: ORF associated with the query gene.
Query.Gene: Common name of the query gene.
Target.ORF: ORF for the array gene.
Target.Gene: Common name of the array gene.
RSA: Random spore analysis
Tetrad: Tetrad dissection

Boeke2006 is an incidence matrix is a 74 by 843 adjacency matrix of the systematic genetic interactions identified between 74 query genes and the deletion gene set in Pan et al.(2004). The row names correspond to the systematic (ORF) names for the 74 query genes. The column names correspond to the systematic (ORF) names of the 843 reporter genes, which showed a synthetic lethal or synthetic sick interaction with at least one query genes. Values are 0 or 1, with a 1 indicating the occurrence of the genetic interaction between the gene pairs.

Source

The data were extracted from Pan et al (2004) and Table S1 of Pan et al. (2006).

Details

In Pan et al (2006), the authors provide this note. Note: SL - synthetically lethal; SF/SL-very severe synthetic fitness defects; SF-obvious but modest synthetic fitness defects; SF (slight) - slight synthetic fitness defect. Approximately 10% of the positive interactions presented here were not scored as positive in the dSLAM screens. These were individually tested because we wanted to make sure that they were indeed false negatives in the dSLAM screens. We also note that there is a small chance that the interactions scored as positive in RSA (random spore analysis) might not reflect direct growth defects of the double mutants but rather, the double mutants are defective in expressing the MFA1pr-HIS3 reporter.

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

Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD. A robust toolkit for functional profiling of the yeast genome. Mol Cell. 2004 Nov 5;16(3):487-96.