Our pipeline uses GADEM [20], which is a good compromise between fully probabilistic and enumerative approaches, can process large sets of ChIP-Seq regions, handles both dimer and monomer motifs, automatically identifies multiple motifs, and automatically adjusts motif widths.
A common strategy in motif interactions is the co-operative binding of multiple motifs and motif-binding domains, which in isolation are somewhat promiscuous, to mediate highly specific interactions.
The cluster in left contains drug-centered motif (red circles) and multiple motifs (purple squares), and the lower cluster in right comprises target-centered motifs and multiple motifs and the upper cluster in right is composed of all four types of motifs.
For clarity, we will explain our method by limiting to only one motif in the sample, and every sequence contains at least one occurrence d-mutant of the motif even though our method can deal with multiple motifs and 10-20% of contamination.
Then, the recall and the precision are computed as A low SN statistic indicates the lack of ability to discover planted multiple motifs and a low PPV statistic can be a signal for less identification accuracy, for instance the occurrence of over- or under-estimates of the planted motif regions.
We use the same approach to adopt traditional promoter scanning to handle multiple motif models and report the smallest p-value over the multiple motif models.
As reported previously, Dilbirligi and Gill [ 37] adopted four different data-mining methods including domain search, individual and multiple motif searches, consensus sequence search, and individual full-length search to mine R-gene-like wheat sequences, and showed that the individual full-length search was the most successful method.
And multiple motif positional co-localization was out of scope of the present study as well.
In the existence of multiple motif hits between a PSSM and a gene, the TFBS with the most significant score was considered as the primary TFBS hit.
Shown are the top five motifs as identified using MEME-ChIP45, which incorporates multiple motif discovery programs such as MEME and DREME.
Each motif model was linked to a transcription factor gene, allowing for redundancies in the motif databases; multiple TFs were allowed to be paired with the same motif, and many TFs were represented by multiple motif models.
