Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites

Bioinformatics. 2003 Oct;19 Suppl 2:ii50-6. doi: 10.1093/bioinformatics/btg1059.


Many cellular signaling pathways induce gene expression by activating specific transcription factor complexes. Conventional approaches to the prediction of transcription factor binding sites lead to a notoriously high number of false discoveries. To alleviate this problem, we consider only binding sites that are conserved in man-mouse genomic sequence comparisons. We employ two alternative methods for predicting binding sites: exact matches to validated binding site sequences and weight matrix scans. We then ask the question whether there is a characteristic association between a transcription factor or set thereof to a particular group of genes. Our approach is tested on genes, which are induced in dendritic cells in response to the cells' exposure to LPS. We chose this example because the underlying signaling pathways are well understood. We demonstrate the benefit of conserved predicted binding sites in interpreting the LPS experiment. Additionally, we find that both methods for the prediction of conserved binding sites complement one another. Finally, our results suggest a distinct role for SRF in the context of LPS-induced gene expression.

Publication types

  • Evaluation Study

MeSH terms

  • Algorithms
  • Base Sequence
  • Binding Sites
  • Chromosome Mapping / methods
  • Conserved Sequence / genetics*
  • Gene Targeting / methods*
  • Molecular Sequence Data
  • Protein Binding
  • Regulatory Elements, Transcriptional / genetics*
  • Sequence Analysis, DNA / methods*
  • Signal Transduction / genetics*
  • Software
  • Transcription Factors / genetics*
  • Transcription, Genetic / genetics*


  • Transcription Factors