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Many of the genes that were downregulated over 3 or 6 hours in the microarray dataset were shown to have putative binding sites for the regulated microRNAs in their 3' UTR.
The dimensions of the microarray dataset were thus 63 (rows) × 1701 (columns).
For the null distribution, 1,000 sets of 158 genes randomly selected from the same microarray dataset were analyzed.
Three genes (TSC22D3, RPL17, and EEF1B2) that were not significant on our microarray dataset were included as negative controls.
Therefore the vectors of 10 genes of each microarray dataset were projected into two dimensions which contain the main variance of the data.
Secondly, genes in the cop1 mutant time course microarray dataset were clustered into 12 expression patterns and overrepresented sequence elements in the upstream of the genes belonged to the same cluster were detected using AlignACE [ 19].
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Complete microarray dataset is available at Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE45423.
SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression), and that each sample represents one unknown point along the progression of that process.
The Microarray dataset are deposited at Gene Expression Omnibus (GEO) database and are accessible through accession number (GSE18762).
The entire microarray dataset is available at http://www.ncbi.nlm.nih.gov/geo/(GSE20431).
The average probe signal for an entire microarray dataset was used to normalize the different samples.
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