Research article
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
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* Corresponding authors: Mats G Gustafsson mg@angstrom.uu.se - Jan Komorowski jan.komorowski@lcb.uu.se
- † Equal contributors
1 The Linnaeus Centre for Bioinformatics, Uppsala University and Swedish University of Agricultural Sciences, Uppsala, Sweden
2 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
3 Department of Engineering Sciences, Uppsala University, Uppsala, Sweden
BMC Systems Biology 2007, 1:45 doi:10.1186/1752-0509-1-45
Published: 16 October 2007Additional files
Additional file 1:
All significant cis-regulatory descriptors (i.e. transcription factor – sequence motif pairs). For each transcription factor and each sequence motif, the three best (p < 0.05) sequence motifs/transcription factors are listed with p-values.
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Additional file 2:
All rules. All rules associating combinations of cis-regulatory descriptors with periodic classes of expression. The p-value for the periodic class that the rule was induced for is given together with the parameters for the the hypergeometric distribution: (N,n,k,x), where N is the number of genes in the data set, n is the number of genes matching the rule, k is the number of genes in the periodic class and x is the number of genes matched by the rule and the periodic class.
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Additional file 3:
All hierarchies of cis-regulatory descriptor combinations. All hierarchies of cis-regulatory descriptor combinations.
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Additional file 4:
Names of the putative sequence motifs. See P# in Figure 5.
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Additional file 5:
The functional signatures of each periodic class. Overrepresentation of function was calculated for a background consisting only of genes detected as periodically expressed in at least one of the experiments. Terms with a two-sided p-value below 0.05 in at least one class are shown.
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