Introduction
Binding site discovery:
-Computational -Experimental
Cis-regulatory evolution
Organisms
-Yeast
-Fly
-Mouse
-Human
Binding site degeneracy
Functional variants
Cis-regulatory code
Regulatory networks

Yeast
Databases and datasets
YEASTRACT - curated repository of more than 12500 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae
SCPD : Yeast Promoter Database

Primary literature
2004
A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation. A. Tanay, I. Gat-Viks and R. Shamir. Genome Research

2000
Computational identification of cis –regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. JD Hughes, PW Estep, S Tavazoie and GM. ChurchJ. Mol.Biol