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A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

Figure 3

Motif network and DNA-binding domain phylogeny for the ZFC4-NR class.

(A) Motif network of nuclear receptor motifs with colors indicating clusters extracted by MCL. (B) Phylogeny of nuclear receptor DNA-binding domains represented by matrices in the motif network. Branch colors correspond to MCL clusters in A. (C) Motif logos were generated using WebLogo [33] for binding sites of NR3C proteins (top), estrogen receptor (middle), and nuclear receptors from other families (bottom). The half-site logos illustrate that estrogen receptor motifs were correctly clustered separately from NR3C matrices and with the other nuclear receptors.

Figure 3