Computational discovery of gene modules and regulatory networks

  title={Computational discovery of gene modules and regulatory networks},
  author={Ziv Bar-Joseph and Georg K. Gerber and Tong Ihn Lee and Nicola J. Rinaldi and Jane Y Yoo and François Robert and D. Benjamin Gordon and Ernest Fraenkel and Tommi S. Jaakkola and Richard A. Young and David Kenneth Gifford},
  journal={Nature Biotechnology},
We describe an algorithm for discovering regulatory networks of gene modules, GRAM (Genetic Regulatory Modules), that combines information from genome-wide location and expression data sets. A gene module is defined as a set of coexpressed genes to which the same set of transcription factors binds. Unlike previous approaches that relied primarily on functional information from expression data, the GRAM algorithm explicitly links genes to the factors that regulate them by incorporating DNA… CONTINUE READING
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