Computational Biology of Transcription Factor Binding

Volume 674 of the series Methods in Molecular Biology pp 419-441


Computational Methods for Analyzing Dynamic Regulatory Networks

  • Anthony GitterAffiliated withComputer Science Department, Carnegie Mellon University
  • , Yong LuAffiliated withDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School
  • , Ziv Bar-JosephAffiliated withComputer Science Department, Carnegie Mellon University Email author 

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Regulatory and other networks in the cell change in a highly dynamic way over time and in response to internal and external stimuli. While several different types of high-throughput experimental procedures are available to study systems in the cell, most only measure static properties of such networks. Information derived from sequence data is inherently static, and most interaction data sets are measured in a static way as well. In this chapter we discuss one of the few abundant sources for temporal information, time series expression data. We provide an overview of the methods suggested for clustering this type of data to identify functionally related genes. We also discuss methods for inferring causality and interactions using lagged correlations and regression analysis. Finally, we present methods for combining time series expression data with static data to reconstruct dynamic regulatory networks. We point to software tools implementing the methods discussed in this chapter. As more temporal measurements become available, the importance of analyzing such data and of combining it with other types of data will greatly increase.

Key words

Gene expression causality clustering data integration time series