Most genetic mutations are detrimental and can lead to events such as cell transformation or death. Thus, recognizing DNA damage and halting the cell replication process until the damage is repaired is crucial to cell and organism viablity. Significant efforts have been devoted in the last 50 years to elucidating the many pathways by which cells sense and respond to different types of DNA damage, often utilizing S. cerevisiae as a model organism because yeasts are eukaryotic and their gene regulation and biochemical pathways involved in responding to DNA damage are expected to be similar to those found in humans. In recent years, the proliferation of spotted and oligonucleotide microarrays has enabled the genome-wide analysis of S. cerevisiae gene transcription in response to multiple DNA damaging agents. In this work, we used oligonucleotide microarrays to quantify the transcriptional response of S. cerevisiae cells to multiple doses (varying over three orders of magnitude) of methyl methanesulfonate (MMS), a DNA-alkylating agent, and gamma radiation (g-ray) in an attempt to show how the global transcriptional response varies with dose and to uncover novel cellular responses to different magnitudes of DNA damage. The transcriptional response was rapid and widespread, with over 1300 genes showing statistically significant modulation to at least one DNA damage treatment. Hierarchical clustering identified several dose-dependent expression patterns and many interesting insights into the pathways involved in the DNA damage response. For example, several ergosterol synthesis genes were regulated in response to MMS but not g-ray. One of the most prominent DNA damage response pathways, Mec1p pathway, was found to be highly induced at intermediate doses of MMS, but its response was subdued at the highest MMS dose tested. Analyzing the dose-dependent changes in genome-wide transcription in response to DNA damage enables the identification of cellular responses that are modulated with dose, providing new insights into how a cell deals with genotoxicity.