Fig 1.
A typical analysis involves submitting gene sets for scanning against known TF models, followed by the identification of sites that are statistically enriched relative to a submitted background gene list.
Fig 2.
The scan and enrichment algorithms produce a graphical display of the TFBS locations on the sequences. There are many options to edit the images, including adjusting the deficit and P-value thresholds for displaying TFBSs, selecting or removing TFs to be viewed, editing the colour scheme for TFs and rearranging the order of the sequences.
Fig 3.
CiiiDER enrichment results for the breast cancer metastasis dataset.
The data are derived from the proportion of regions bound for each TF, which is the number of bound regions divided by the total number of regions. The plot shows the enrichment (ratio of proportion bound) and average log proportion bound. Size and colour show ∓log10(P-value) (significance score); it is greater than zero if the TF is over-represented and less than zero if under-represented. Underlying data are provided in S1 Data.
Fig 4.
Phylogenetic conservation of TF binding sites in the IFNβ promoter.
The results of the enrichment algorithm, displaying the ten most significantly enriched TFs present in at least half of the promoters. Underlying data are provided in S3 Data.