BMC Genomics 2008, 9:627 http://www.biomedcentral.com/1471-2164/9/627 and helped draft the manuscript. MTK assisted with the microarrays and the statistical and clustering analyses. PVB participated in the design of the study, the growth of strains, collection of RNA, interpretation of the clustering analyses, and drafting the manuscript. KEK conceived the study, participated in its design and coordination, and helped to draft the manuscript. All authors read and approved the final manuscript. Additional material Additional file 1 Transcription-factor consensus binding sequences (TFMs). The table lists the 2,892 transcription-factor consensus binding sequences (TFMs) compiled from both experimental and comparative phylogenic studies that were used for calculating the feature configuration statistic (FCS). Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S1.xls] Additional file 2 Assessment of clustering quality using the feature configuration sta- tistic (FCS) and consensus share (CS) for genes that significantly responded to anaerobiosis (N2), antimycin A treatment in air (antimycin A + air), and anaerobiosis in the presence of antimycin A (N2 + antimycin A). The temporal profiles of genes that responded signif- icantly (P < 0.01) to each treatment were separately clustered 10 times using Kohonen's SOM algorithm with 1-D string topology and Pearson correlation as the distance metric. The average FCS P value (solid line, left ordinate) for 2,892 transcription-factor consensus binding sequences (TFMs) and CS (dotted line, right ordinate) are plotted as a function of cluster number (K). Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S2.jpeg] Additional file 3 Abridged list of TFMs, MDscan sequence logos, and MIPS functional categories significantly enriched from clustering the genomic responses to each treatment. The tables provide an overview of consensus sequence motifs (TFMs), MDscan sequence logos, and MIPS functional categories that were significantly (p < 0.01) enriched from clustering the genomic responses to anaerobiosis (A), antimycin A treatment under nor- moxia (B), and antimycin A treatment under normoxia (C). See addi- tional files 4, 5, 6 for unabridged listings. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S3.doc] Additional file 4 Unabridged list of TFMs and MIPS functional categories that were significantly (P < 0.01) enriched from clustering the 1754 genes that were differentially (P < 0.01) expressed in response to anaerobiosis in galactose medium. The data are for the wild-type strain over 3 genera- tions of anoxia. SOM clustering was used with K = 13. Genes that are contained in each of the clusters presented in Figure 3A in the manuscript are provided in the "Gene-Cluster Membership" worksheet. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S4.xls] Additional file 5 Unabridged list of TFMs and MIPS functional categories that were significantly (p < 0.01) enriched from clustering the 901 genes that were differentially (p < 0.01) expressed in response antimycin A treat- ment under normoxia in galactose medium. The data are for the wild- type strain over 3 generations following antimycin A treatment in air. SOM clustering was used with K = 6. Genes that are contained in each of the clusters presented in Figure 3B in the manuscript are provided in the "Gene-Cluster Membership" worksheet. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S5.xls] Additional file 6 Unabridged list of TFMs and MIPS functional categories that were significantly (p < 0.01) enriched from clustering the 669 genes that were differentially (p < 0.01) expressed in response antimycin A treat- ment under anoxia in galactose medium. The data are for the wild-type strain over 3 generations of anoxia following a 3-generation treatment with antimycin A in air. SOM clustering was used with K = 10. Genes that are contained in each of the clusters presented in Figure 3C in the manuscript are provided in the "Gene-Cluster Membership" worksheet. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S6.xls] Additional file 7 Distribution of regression slopes for genes that were acutely repressed (Figure 1), chronically repressed (Figure 2), acutely induced (Figure 3), and chronically induced (Figure 4) in response to anaerobiosis. The graphs show the distribution of growth-rate slopes for specific gene clusters from the anaerobic dataset (black) in comparison to ESR-induced (red) and ESR-repressed genes (green). The graphs were generated using the online utility http://growthrate.princeton.edu developed by Brauer et al. 2008 [9]. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-627-S7.doc] Acknowledgements This work was supported by National Institutes of Health grant RO1- GM59826 to KEK. References 1. Rep M, Krantz M, Thevelein JM, Hohmann S: The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J Biol Chem 2000, 275:8290-8300. 2. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11:4241-4257. 3. Moskvina E, Schüller C, Maurer CT, Mager WH, Ruis H: A search in the genome of Saccharomyces cerevisiae for genes regulated via stress response elements. Yeast 1998, 14:1041-1050. 4. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA: Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 2001, 12:323-337. 5. Lai LC, Kosorukoff AL, Burke PV, Kwast KE: Dynamical remode- ling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Page 12 of 14 (page number not for citation purposes)