Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation

Additional file 1:

Log₂ fold change data for all arrays. This text file contains the log₂ fold change value for all 6,322 ORFs represented on the NimbleGen™ arrays. There are 18 columns of data, 3 for each MMS dose (0.001%, 0.01%, and 0.1%) and 3 for each γ-ray dose (1 Gy, 10 Gy, 100 Gy).

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Additional file 2:

Average log₂ fold change for all genes with significant transcriptional response to MMS or γ-ray. This EXCEL file contains the log₂ fold change value for all 920 genes with a statistically significant transcriptional response to MMS and/or γ-ray. There are 6 columns of data, 3 with the average log₂ fold change for each dose of MMS and 3 with the average log₂ fold change for each dose of γ-ray. These genes were clustered and shown in Figure 1. Additionally, this file contains the GO annotation assigned to each gene and shown in Figure 7-A.

Format: XLS Size: 196KB Download file

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Additional file 3:

Average log₂ fold change for all genes with a significant transcriptional response to MMS. This EXCEL file contains the log₂ fold change value for all 714 genes with at least a 3-fold transcriptional response to MMS. There are 3 columns of data, each one containing the average log₂ fold change for one dose of MMS. These genes were clustered and shown in Figure 5-A. Additionally, this file contains the GO annotation assigned to each gene and shown in Figure 7-B.

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Additional file 4:

Average log₂ fold change for all genes with a significant transcriptional response to γ-ray. This EXCEL file contains the log₂ fold change value for all 482 genes with at least a 3-fold transcriptional response to γ-ray. There are 3 columns of data, each one containing the average log₂ fold change for one dose of γ-ray. These genes were clustered and shown in Figure 5-B. Additionally, this file contains the GO annotation assigned to each gene and shown in Figure 7-C.

Format: XLS Size: 87KB Download file

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Additional file 5:

MEME system motif analysis results. This EXCEL file contains the 3 enriched motifs identified in the text from Figure 3-D, Figure 4, and Figure 6-B. The columns contain the motif and its E-value as well as the ORF, gene product, and GO annotation for each gene associated with the enriched region.

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Additional file 6:

GO analysis of clusters presented in Figure 5. This figure contains the results of gene ontology analysis of the clusters presented in Figure 5. (A) genes induced by MMS, (B) genes repressed by MMS, (C) genes induced by γ-ray, and (D) genes repressed by γ-ray. Genes are sorted according to their GO biological process annotation and can be viewed in Additional Files 3 (MMS) and 4 (γ-ray).

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Additional file 7:

Cell viability after exposure to DNA-damaging agent. This table shows the percentage of Saccharomyces cerevisiae cells living one hour after exposure to the DNA damage caused by MMS or γ-ray. Viability was determined by flow cytometry quantifying the percentage of cells excluding propidium iodide.

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