Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles

Bioinformatics. 2003 Nov 22;19(17):2321-2. doi: 10.1093/bioinformatics/btg307.


Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that uses self-organizing maps to translate high-dimensional expression profiles of time courses or sample classes into animated, coherent and robust mosaics images. GEDI facilitates identification of interesting patterns of molecular activity simultaneously across gene, time and sample space without prior assumption of any structure in the data, and then permits the user to retrieve genes of interest. Important changes in genome-wide activities may be quickly identified based on 'Gestalt' recognition and hence, GEDI may be especially useful for non-specialist end users, such as physicians.

Availability: GEDI v1.0 is written in Matlab, and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at

Supplementary information:

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Computer Graphics*
  • Database Management Systems*
  • Databases, Genetic
  • Gene Expression Profiling / methods*
  • Information Storage and Retrieval / methods*
  • Software*
  • Systems Integration
  • Time Factors
  • User-Computer Interface*