Table 1

Definition of positive and negative sets of matrix matches

Criterion

Gal4p

Rpn4p


Unique specificity

Spacer of 11 bp [50]

Atypical zinc finger [42]

Well characterized specificity

Protein-DNA co-crystal [51]

Large number of binding sites, low degeneracy [42]

Well characterized target gene set

Classic genetic system [52] and high-throughput studies [45,46]

Targets include almost all proteasomal subunits [42] stereotypical expression pattern [48]


Criteria used to define positive and negative sets to use in this study. It is important to avoid factors whose specificity overlaps with other factors, because binding sites that are not occupied by one factor may be constrained because of binding by another, and to choose factors with characterized specificity because our methods rely on the assumption that the specificity is known.

Moses et al. Genome Biology 2004 5:R98   doi:10.1186/gb-2004-5-12-r98

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