Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets

Table 3 Gene ranks predicted by SSEM-Lasso for corresponding yeast genetic deletion microarray experiments

Microarray experiment	Gene target	Rank with original compendium	Rank with modified compendium
erg11Δ/ERG11 ¹	ERG11	277	301
erg6Δ ¹	ERG6	1	1
spt3Δ ²	SPT3	5	47
hem1Δ ³	ERG5	40	41

¹Christadore, L. Boston University. 2012.
²James, N., et al. Genetics 177:123 2007 [60].
³Protchenko O., et al. Eukaryot. Cell 7:859 2008 [59].
SSEM-Lasso gene ranks were determined for gene targets of genetic deletions and compound treatments. All microarray experiments were performed using Affymetrix Yeast Genome 98 gene chips, and data was RMA-normalized before processing with SSEM-Lasso algorithm. The original and modified training networks (modified with corresponding gene target expression data only) were used to determine ranks of target genes for each experiment. Raw data was obtained from published experiments (GEO) or conducted in in-house, as indicated in footnotes. Average ranks for duplicate experiments are shown.

ISSN: 1752-0509