Supplementary information
FROM:
Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression
Larsson Omberg, Joel R Meyerson, Kayta Kobayashi, Lucy S Drury, John F X Diffley & Orly Alter
doi:10.1038/msb.2009.70
BACK TO ARTICLEGeneral supplementary information
Supplementary Information
Supplementary Text; Supplementary Figures 1–12; Supplementary Tables I–II
Mathematica Notebook (a)
A Mathematica 5.2 code file, executable by Mathematica 5.2 and readable by Mathematica Player, freely available at http://www.wolfram.com/products/player/.
Mathematica Notebook (b)
A PDF format file, readable by Adobe Acrobat Reader.
Dataset 1
A tab-delimited text format file, readable by both Mathematica and Microsoft Excel, tabulating relative mRNA expression levels of 4771 probes of the UT DNA microarrays that correspond to the K=4270 genes across 24 samples.
Dataset 2
A tab-delimited text format file, readable by both Mathematica and Microsoft Excel, tabulating relative mRNA expression levels of 8540 probes of the WU DNA microarrays that correspond to the K=4270 genes across 72 samples.
Dataset 3
A tab-delimited text format file, readable by both Mathematica and Microsoft Excel, tabulating 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.
Dataset 4
A tab-delimited text format file, readable by both Mathematica and Microsoft Excel, reproducing descriptions and genomic coordinates [Nieduszynski et al, 2007] of the 325 confirmed ARSs in Saccharomyces cerevisiae.
Dataset 5
A tab-delimited text format file, readable by both Mathematica and Microsoft Excel, reproducing cell cycle annotations [Spellman et al, 1998], DNA damage responses [Jelinsky and Samson et al, 1999], descriptions and genomic coordinates [Cherry et al, 1997] and of the 4270 Saccharomyces cerevisiae genes.
Dataset 6
A tab-delimited text format file, readable by both Mathematica and Microsoft Excel, tabulating 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.
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