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Activated Signal Transduction Kinases Frequently Occupy Target Genes

Study Design

Data Insights Supplemental Material

Acknowledgements

Data Analysis

Analysis of genome-wide binding occupancy with transcriptional activity

To correlate binding of Tpk1 and Tpk2 with the transcriptional rates of genes, the 5,324 genes for which transcription rates were available were divided into five classes according to their transcriptional rate (Holstege et al. 1998, Pokholok et al. 2005). Each ORF was assigned a fixed length and subdivided into forty equal regions. Probes on the array were then assigned to the nearest corresponding relative position. Probes in promoter regions were similarly assigned following subdivision into twenty regions. The average enrichment then calculated across the promoter and gene for each of the five transcription classes. A plot of the results is shown in Figure 3C.


Comparison of kinase and transcription factor binding

To compare the genes bound by each kinase with those bound by each transcription factor (Harbison et al. 2004), we performed a hypergeometric distribution test, testing the likelihood of the observed overlap or higher. Supplemental Table S7 displays the significant associations, which are still highly significant after correction for multiple testing.
 
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