Vertebrate motif clusters v3.0

# Vertebrate motif clusters from cis-bp Current version: 3.0 All the motif information is based on the cis-bp database described in (Weirauch et al., 2014)[http://dx.doi.org/10.1016/j.cell.2014.08.009]. Motif information was downloaded from cis-bp (http://cisbp.ccbr.utoront/o.ca/; retrieved Oct 2014). Vertebrate motifs were selected based on the following list of species: Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Tetraodon nigroviridis, Xenopus laevis, Xenopus tropicalis, Gallus gallus, Meleagris gallopavo, Anolis carolinensis, Monodelphis domestica, Takifugu rubripes, Oncorhynchus tshawytscha, Gasterosteus aculeatus, Ornithorhynchus anatinus, Sus scrofa, Cavia porcellus, Oryctolagus cuniculus, Pan troglodytes, Taeniopygia guttata. Only motifs with direct evidence of binding in any of these species were selected. Within every motif family, as annotated by cis-bp, all motifs were clustered using 'gimme cluster' from the GimmeMotifs package (Heeringen and Veenstra, 2011)[http://github.com/simonvh/gimmemotifs] with a threshold of 0.9999. The cluster motif names are annotated with the motif family name. Any name containing 'Average' is a unique yet arbitrary name of a specific cluster of motifs. The annotation of motifs to factors and vice versa is based on the annotation of human, mouse and Xenopus tropicalis proteins from the cis-bp annotation and includes direct as well as inferred motifs. This is an aggregate over these three species, and might be incomplete. For more (species-)specific annotation, see the file 'TF_Information_all_motifs.txt' that can be obtained from cis-bp.