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

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Received:

18 February 2003

Revision received:

11 April 2003

Published:

22 November 2003

Cite

Gabriel S. Eichler, Sui Huang, Donald E. Ingber, Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles, Bioinformatics, Volume 19, Issue 17, November 2003, Pages 2321–2322, https://doi.org/10.1093/bioinformatics/btg307
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Abstract

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

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Author notes

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

© Oxford University Press 2003; all rights reserved.

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