This site supports a paper published in PLoS computational Biology on 29 Feb 2008



Transcription map:

Condition dependant
transcription factors

Supplementary Tables:

Our motif clustering & comparison method

Motif comparison and clustering:
In this example, the initial set consists of four motifs. The score assigned to each pair of motifs is the score of the best possible alignment between them (including the reverse complement form, as demonstrated in this example). In each step the highest scoring pair is merged into a new motif (by combining the evidence from both motifs). These steps are repeated until we are left with a single motif. The order of merge operations results in a tree, where the leaves are the initial motifs. Each frontier in this tree creates a set of motifs. A frontier in a tree is a subset of nodes, non-descendent to each other, that every leaf in the tree is a descendant of one of them. In this example, a frontier resulting in two motifs is chosen, one is an initial motif and the other is a motif created by merging three initial motifs. These two motifs are the non-redundant set of motifs, derived from the initial set.