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Bioinformatics Vol. 19 no. 17 2003
pages 2321-2322
© 2003 Oxford University Press

Applications Note

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

Gabriel S. Eichler , Sui Huang and Donald E. Ingber *

Vascular Biology Program, Departments of Pathology and Surgery, Children's Hospital/Harvard Medical School, Boston, MA 02115, USA

Received on February 18, 2003 ; revised on April 11, 2003 ; accepted on May 27, 2003

Summary: 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 http://www.chip.org/~ge/gedihome.html

Supplementary information: http://www.chip.org/~ge/gedihome.html

Contact: donald.ingber{at}tch.harvard.edu

* To whom correspondence should be addressed.


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