Cancer Institute A national cancer institute
designated cancer center

Atul Butte

Publication Details

  • Comparing the similarity of time-series gene expression using signal processing metrics JOURNAL OF BIOMEDICAL INFORMATICS Butte, A. J., Bao, L., Reis, B. Y., Watkins, T. W., Kohane, I. S. 2001; 34 (6): 396-405

    Abstract:

    Many algorithms have been used to cluster genes measured by microarray across a time series. Instead of clustering, our goal was to compare all pairs of genes to determine whether there was evidence of a phase shift between them. We describe a technique where gene expression is treated as a discrete time-invariant signal, allowing the use of digital signal-processing tools, including power spectral density, coherence, and transfer gain and phase shift. We used these on a public RNA expression set of 2467 genes measured every 7 min for 119 min and found 18 putative associations. Two of these were known in the biomedical literature and may have been missed using correlation coefficients. Digital signal processing tools can be embedded and enhance existing clustering algorithms.

    View details for DOI 10.1006/jbin.2002.1037

    View details for Web of Science ID 000177556700003

    View details for PubMedID 12198759

Stanford Medicine Resources:

Footer Links: