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Journal of Biomedicine and Biotechnology
Volume 2006 (2006), Article ID 69141, 11 pages
http://dx.doi.org/10.1155/JBB/2006/69141
Research Article

Towards a Holistic, Yet Gene-Centered Analysis of Gene Expression Profiles: A Case Study of Human Lung Cancers

1Vascular Biology Program, Department of Surgery, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
2Bioinformatics Program, Boston University, Boston, MA 02215, USA
3Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, MD 20892, USA

Received 2 June 2006; Revised 14 August 2006; Accepted 25 August 2006

Copyright © 2006 Yuchun Guo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Genome-wide gene expression profile studies encompass increasingly large number of samples, posing a challenge to their presentation and interpretation without losing the notion that each transcriptome constitutes a complex biological entity. Much like pathologists who visually analyze information-rich histological sections as a whole, we propose here an integrative approach. We use a self-organizing maps-based software, the gene expression dynamics inspector (GEDI) to analyze gene expression profiles of various lung tumors. GEDI allows the comparison of tumor profiles based on direct visual detection of transcriptome patterns. Such intuitive “gestalt” perception promotes the discovery of interesting relationships in the absence of an existing hypothesis. We uncovered qualitative relationships between squamous cell tumors, small-cell tumors, and carcinoid tumor that would have escaped existing algorithmic classifications. These results suggest that GEDI may be a valuable explorative tool that combines global and gene-centered analyses of molecular profiles from large-scale microarray experiments.