SCOPE Glossary

Some handy definitions:

• Regulon: a set of genes that are co-regulated at the level of transcription, and contain a known biologically defined cis-regulatory element.

• Motif: a collection of putative binding sites, represented as (for example) a consensus sequence, a position weight matrix, or a sequence logo.

• Transcription Factor Binding Site: an unambiguous DNA-word that marks the spot at which a transcription factor has been shown to bind DNA.

• cis-Regulatory element: a list of binding sites for a transcription factor (these are usually words which look similar to each other). May be represented as a Position Weight Matrix or a consensus.

• Position Weight Matrix: A matrix where every column contains the number of times in the reported sites that a particular base was A, T, C, or G. (Other versions of PWMs record probabilities or log-likelihoods, our version records raw counts).

• Consensus: A compact representation using an extended IUPAC alphabet to denote degenerate positions (for example, A/T= W, A/C= M, A/T/C= H). Thus the motifs ATAA and AATA will be represented with a consensus of AWWA. This consensus expands to two other motifs that weren’t included in the original list (ATTA and AAAA). This is an example of how confusing the summary representation with the actual list of sites can get you into trouble.