Mining ChIP-chip data for transcription factor and cofactor binding sites

@article{Smith2005MiningCD,
  title={Mining ChIP-chip data for transcription factor and cofactor binding sites},
  author={Andrew D. Smith and Pavel Sumazin and Debopriya Das and Michael Q. Zhang},
  journal={Bioinformatics},
  year={2005},
  volume={21 Suppl 1},
  pages={
          i403-12
        }
}
MOTIVATION Identification of single motifs and motif pairs that can be used to predict transcription factor localization in ChIP-chip data, and gene expression in tissue-specific microarray data. RESULTS We describe methodology to identify de novo individual and interacting pairs of binding site motifs from ChIP-chip data, using an algorithm that integrates localization data directly into the motif discovery process. We combine matrix-enumeration based motif discovery with multivariate… CONTINUE READING

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