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

Binding site degeneracy
Degenerate variants are nucleotide variants at a particular position in a TF binding site motif that do not alter the regulatory effect of the binding site, resulting in equivalent expression of target genes.

Primary literature
Luscombe, N. M., and J. M. Thornton. 2002. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320:991-1009.

Mirny, L. A., and M. S. Gelfand. 2002. Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res 30:1704-1711.

Moses, A. M., D. Y. Chiang, M. Kellis, E. S. Lander, and M. B. Eisen. 2003. Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol 3:19.

Tagle, D. A., B. F. Koop, M. Goodman, J. L. Slightom, D. L. Hess, and R. T. Jones. 1988. Embryonic epsilon and gamma globin genes of a prosimian primate Galago crassicaudatus. Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol 203:439-455.

Databases and datasets
In progress...

Software and tools
In progress...

Labs
In progress...