Following is the list of expression datasets we analyzed in our study, and links to the web-sites from which they can be downloaded (full citations and statistics for each dataset are given in the Supplemental Notes of our manuscript):

• Human cell cycle
  Whitfield et al., Mol Biol Cell 2002
  http://genome-www.stanford.edu/Human-CellCycle/HeLa
  
  
• Mouse innate immune response
  Gilchrist et al., Nature 2006
  http://www.systemsbiology-immunity.org
  (Macrophage and RAW 264.7 cells)
  
  
• Yeast HOG MAPK pathway
  O'Rourke and Herskowitz, Mol Biol Cell 2004
  http://www.molbiolcell.org/cgi/content/full/E03-07-0521/DC1
  
  
• Human and mouse tissue atlas
  Su et al., PNAS 2004
  http://wombat.gnf.org/index.html
  (Human U133A + GNF1H and Mouse GNF1M, gcRMA-condensed)
  
  
• Fly development
  
  1. Emryogenesis: Hooper et al., Mol Syst Biol 2007
     GEO (series GSE6186)
  2. Life cycle: Arbeitman et al., Science 2002
     SMD (search under Drosophila development, time course)
  3. Embryo and adult samples: Spellman and Rubin, J Biol 2002
     http://jbiol.com/content/1/1/5/additional/
  
  
• Human stem cells
  Mueller et al., Nature 2008
  GEO (series GSE11508)