High-resolution time course analysis of gene expression from pituitary

Cold Spring Harb Symp Quant Biol. 2007;72:381-6. doi: 10.1101/sqb.2007.72.011.

Abstract

In both the suprachiasmatic nucleus (SCN) and peripheral tissues, the circadian oscillator drives rhythmic transcription of downstream target genes. Recently, a number of studies have used DNA microarrays to systematically identify oscillating transcripts in plants, fruit flies, rats, and mice. These studies have identified several dozen to many hundred rhythmically expressed genes by sampling tissues every 4 hours for 1, 2, or more days. To extend this work, we have performed DNA microarray analysis on RNA derived from the mouse pituitary sampled every hour for 2 days. COSOPT and Fisher's G-test were used at a false-discovery rate of less than 5% to identify more than 250 genes in the pituitary that oscillate with a 24-hour period length. We found that increasing the frequency of sampling across the circadian day dramatically increased the statistical power of both COSOPT and Fisher's G-test, resulting in considerably more high-confidence identifications of rhythmic transcripts than previously described. Finally, to extend the utility of these data sets, a Web-based resource has been constructed (at http://wasabi.itmat.upenn.edu/circa/mouse ) that is freely available to the research community.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Circadian Rhythm / genetics*
  • Circadian Rhythm / physiology*
  • Computational Biology
  • Databases, Genetic
  • Gene Expression
  • Gene Expression Profiling / statistics & numerical data
  • Internet
  • Mice
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Pituitary Gland / physiology*
  • Time Factors