Supplemental material for L. Omberg, J. R. Meyerson, K. Kobayashi, L. S. Drury, J. F. X. Diffley and O. Alter, "Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression," Nature Molecular Systems Biology 5, article 312 (October 2009). To read the press release, go to: http://www.engr.utexas.edu/news/articles/200910131769/.
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Nature_MSB_2009.pdf
A PDF format file of Supplementary information Sections, Figures and Tables, readable by Adobe Acrobat Reader.
Nature_MSB_2009_Supplementary_Information.pdf
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Yeast mRNA Expression Data

Relative mRNA expression levels of 4771 probes of the University of Texas (UT) DNA microarrays that correspond to the K=4270 genes across 24 samples.
Relative mRNA expression levels of 8540 probes of the Washington University (WU) DNA microarrays that correspond to the K=4270 genes across 72 samples.
The averaged log2 of the relative mRNA expression of the K=4270 genes across the L=12 time points and across the M=3 conditions of Mcm2-7 origin binding. The genes are sorted by their angular distances between the second and third HOSVD combinations (Supplementary information Section 2.6 and Dataset 6), which represent the unperturbed cell cycle expression oscillations (Figure 2 and Supplementary Figure 12). The angular distance of each gene is also listed.

Annotations of Yeast ARSs and Genes

Descriptions and genomic coordinates of the 325 confirmed ARSs in Saccharomyces cerevisiae reproduced from the Replication Origin Database (OriDB), Nieduszynski et al, 2007.
Cell cycle annotations of the 4270 yeast genes reproduced from Spellman et al, 1998, DNA damage responses reproduced from Jelinsky and Samson, 1999, and descriptions and genomic coordinates reproduced from the Saccharomyces Genome Database (SGD), Cherry et al, 1997.

Selected Eigenarrays and Superpositions of Eigenarrays

The eigenarrays and superpositions of eigenarrays that define the global gene expression patterns of the seven significant and unique subtensors of the averaged data cuboid. The expression levels of the genes in the intersections of the fourth through seventh HOSVD combinations, as computed by using the corresponding eigenarrays, are also tabulated. The ten significant among the 1294 genes that are underexpressed in the fourth and overexpressed in the fifth and sixth combinations are enriched in histone genes. The 100 significant among the 1412 genes that are overexpressed in the fourth and underexpressed in the fifth and seventh combinations are enriched in genes with ARSs near their 3' ends.