Analysis of Transcription-Factor Binding-Sites. To rationalize the observed patterns of species-dependent and species-independent expression we performed two separate transcription-factor binding-site analyses. A) We employed a library-based position-weight matrix enrichment analysis using the JASPAR library and the clover algorithm. We separately tested rat (rows with yellow boxes) and mouse (rows with blue boxes) promoter sequences from rat-specific, mouse-specific, and common genes. Thus the first row indicates the analysis of the promoter sequences of the rat orthologs of genes displaying mouse-specific TCDD expression. Each column represents a separate position-weight matrix, and only matrices enriched or depleted in at least two datasets are included. The colour bar indicates the p-value based on 10,000 randomizations. B) and C) We also performed de novo motif discovery using the MotifSampler algorithm. Two matrices enriched in genes showing species-independent responses to TCDD were converted into sequence logos and are displayed here. Neither sequence appears to match a known transcription-factor binding-site.