Of these, 46 (0.73% of the yeast proteome) were defined as strong candidates, either being detected using the canonical-motif scoring method, or scoring above the upper cutoff using PSSM-motif method.
In cases these assumptions are violated even when potential outliers are removed (outliers being detected using the Bonferroni outlier test), Box-Cox transformations were performed, after which assumptions were met in all instances.
Once again, CGHScan identified the same eight known deletions, as well as other putative variable regions, with more overall regions being detected using the less stringent cutoff (data not shown).
Using BD LSR II, JC-1 stain was excited with 488 nm blue laser with green fluorescence being detected using the 505LP 525/50BP filter, whereas red fluorescence was detected using the 570LP 585/42BP filter.
In addition to identifying eight of the nine known deletions, many additional putative variable regions were identified using either cutoff, with more regions being detected using the less stringent cutoff.
In the detection of negative interactions, the intermediate rank product showed consistently the best results among all the data pairs, making it an appropriate rank aggregation function in case both positive and negative interactions are being detected using the same setup.
