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

Cis-regulatory evolution

Software and tools
ESPERR evolutionary and sequence pattern extraction through reduced representation
Sockeye has been developed with a focus on displaying potential gene regulatory regions and for running and visualising the results from regulatory element detection approaches and algorithms.

Databases and datasets
cis RED The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations.

Primary literature
2006
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh SD, True JR, Carroll SB. Nature.

Cis-regulatory evolution of Chalcone-synthase expression in the genus Arabidopsis. de Meaux J, Pop A, Mitchell-Olds T. Genetics

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

2005
Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG, Hartl DL. Genetics

2004
cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes, C Castillo-Davis, D Hart, G. Achaz. Genome Research

2002
Abundant Raw Material for Cis-Regulatory Evolution in Humans, MV. Rockman and GA. Wray. Molecular Biology and Evolution