Results from example 3 – Genes responding to forskolin treatment. Results from the forskolin-analysis output in HTML format. The table is a combination of results from four different analyses performed in MotifLab. The “total”, “support” and “p-value” columns are from an analysis that counts the number of times each motif occurs in the sequences and estimates the significance of overrepresentation (significant p-values are highlighted in red). The “conservation” column is the average score taken from an analysis that compares the binding sites for each motif to a selected numeric feature (here conservation). The “kurtosis” and “histogram” columns are from an analysis of the positional distribution of the binding sites for each motif. The “group” column is from an analysis that compares the number of binding sites for each motif within sequences from two different groups to see if some motifs are overrepresented in one group compared to the other. Here we compared the group of upregulated genes to the downregulated genes. Motifs in the “A” and “B” groups (in red) were significantly overrepresented in the upregulated sequences whereas motifs in the “D” group (in green) were overrepresented in the downregulated sequences. Motifs in the “C” group (yellow) occurred at approximately the same rates in both groups. The table is sorted according to the combined ranks of p-values (ascending), conservation (descending) and kurtosis (descending). Note that almost all top ranking motifs are preferentially located within a narrow region upstream of the TSS, as indicated by the sharp peaks in the histograms around this position. Motif types are colour coded in the left-most column (CREB/ATF motifs with boxes in red, SP1 in blue, NF-Y in yellow, nuclear respiratory factors in green, others in grey).
Klepper and Drabløs BMC Bioinformatics 2013 14:9 doi:10.1186/1471-2105-14-9