Activated Signal Transduction Kinases Frequently Occupy Target Genes

Study Design

• Reagents
• Technology
• Location Analysis Protocols
• Data Processing
• Normalization and Analysis
• Identification of Bound Regions
• Error Rates
• Controls

• Download Location Data
• Data Analysis

• MAPK
  • Hog1
  • Fus3 and Kss1
  • Slt2 and Smk1
• Protein Kinase A
  • Tpk 1
  • Tpk 2

• Supplemental Figures
• Supplemental Tables

We used GenePix software (Axon) to obtain background-subtracted intensity values for each fluorophore for every feature on the array. We normalized the intensities in the IP-enriched channel to intensities in the genomic DNA channel using the median values of the dataset. We then used a single chip error model (Hughes et al., 2000) to calculate confidence values for each spot on each array (single probe p-value). This error model functions by converting the intensity information in both channels to an X score which is dependent on both the absolute value of intensities and background noise in each channel.

Replicate data were combined, using the X scores and ratios of individual replicates to weight each replicate's contribution to a combined X score and ratio. The X scores for the combined replicate are assumed to be normally distributed which allows for calculation of a p-value for the enrichment ratio seen at each feature.