Problems:

Too much false positives (specifity) due to:

• Binding sites patterns are very short (5-15 bp)
• Usage of TF databases: bias (new patterns)
• Relationships between TFs are complex and degenerated

There is room for the improvement...

• Genome-wide expression data from microarrays
• Phylogenetic information from homologous genes
• New research about epigenetic information, CpG islands, DNA bendability, modules (cooperative sites)