Yeast data sources

Three protein-DNA interaction sources were used:

• YPD
• Osmotic stress
• Rapamycin

The Science Signaling Database of Cell Signaling model of the High Osmolarity Glycerol pathway was used to select the HOG sources (registration required). The TOR sources were obtained from Zaman et al

Three time series gene expression datasets were used:

• Short osmotic stress dataset
• Long osmotic stress dataset
• TOR

The HOG gold standard and osmotic stress evidence was composed of the following data:

• KEGG high osmolarity MAPK signaling pathway
• Science Signaling Database of Cell Signaling HOG pathway
• Hohmann et al HOG pathway
• Hohmann HOG pathway
• Krantz et al HOG pathway
• de Nadal and Posas HOG pathway
• Rodríguez-Peña et al HOG pathway
• Hillenmeyer et al screen
• Saccharomyces Genome Database genes annotated with the decreased resistance to hyperosmotic stress phenotype

The TOR extended gold standard used the following sources:

• Zaman et al TOR pathway
• TOR signaling cascade GO annotation
• Chan et al screen
• Xie et al screen
• Hillenmeyer et al screen
• Saccharomyces Genome Database genes annotated with a rapamycin-related phenotype

Please see the experimental validation page for our new osmotic stress results.

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