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

List of Strains
Supplemental Table S1

Genes Bound by Kinases
Supplemental Table S2
Supplemental Table S3
Supplemental Table S4
Supplemental Table S5
Supplemental Table S6
Tables S2-S5 show all genes that were occupied by different signaling molecules by Chip-chip experiments. Bound genomic probes were determined by a genomic peak finding algorithm (see Genome-wide ChIP-chip analysis). Bound probes were combined into regions, if possible, and the maximum binding ratio, as well as number of probes spanning the regions, were calculated. Bound regions were assigned to the closest gene, by first testing whether it overlaps with the transcriptional start site of genes (TSS overlap) and second with the transcribed portion of the gene (gene overlap). If neither approach identified a gene, the closest gene is assigned and the distance in bp (proximity) is indicated.

Overlap with Transcription Factors
Supplemental Table S7
Genes bound by the kinases Hog1p, Fus3p, Kss1p, Ste5p and Tpk2p were systematically compared to the genes bound by transcriptional regulators as determined by Harbison et al. (P < 0.001). The overlap between the kinase targets and the regulator targets was evaluated by a hypergeometric test, revealing the likelihood of detecting the observed number of overlapping genes or higher by chance alone. Genes for which data were available in both the kinase and the regulator experiment were used for calculation.