St. Jude Research
Department of Biostatistics

Agreement of differential expression (AGDEX)

  • We have developed a statistical procedure to evaluate agreement of differential expression (AGDEX) for cross-species genomics. Johnson et al (2010) used AGDEX to show that the transcriptome of a model brain tumor in mice shows statistically significant similarity to that of a subtype of the human brain tumor ependymoma. Gibson et al (2010) published a similar result for a subtype of the human brain tumor medulloblastoma.  The AGDEX method is described in the Supplementary Methods of Johnson et al. (2010).
  • The method is implemented as a package for the freely available R statistical computing software.
  • To install AGDEX:
    • Download AGDEX_1.0.1.zip and execute the command install.packages(“download.dir/AGDEX_1.01.zip”,repos=NULL) in R, where download.dir is the directory to which the file was saved.
    • Alternatively, one may download AGDEX_1.0.1.tar.gz, and execute the command install.packages(“download.dir/AGDEX_1.0.1.tar.gz”,type=”source”,repos=NULL) in R. After executing install.packages, execute library(AGDEX) to make the package available for use in your R session.
    • The AGDEX user’s manual explains how to use the AGDEX package. '
  • To receive alerts regarding software updates, send an e-mail with "Updates on AGDEX Software" in the subject line.
  • More questions? Contact Stan Pounds.