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

Mouse

Primary literature
2000
Human-mouse genome comparisons to locate regulatory sites WW. Wasserman, , M. Palumbo, W. Thompson, JW. Fickett & CE. Lawrence. Nature Genetics

Software and tools
CisView - a browser of mouse regulatory motifs and regions in the genome.
TRANSPro systematic promoter analysis of co-regulated genes. Known transcription factor binding sites are indicated.

Databases and datasets
TRED- Transcriptional Regulatory Element Database, an integrated repository for both cis- and trans- regulatory elements in mammals
TRRD- hierarchical organization of transcription regulatory regions of eukaryotic genes.
TRANSCompel is a specialized database module on composite regulatory elements.
TRANSFAC comprises extensive information on transcription factors and their structures, functions, expression patterns