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

Guo, Yuchun; Eichler, Gabriel S.; Feng, Ying; Ingber, Donald E.; Huang, Sui

doi:https://doi.org/10.1155/JBB/2006/69141

BioMed Research International

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Research Article | Open Access

Volume 2006 | Article ID 069141 | https://doi.org/10.1155/JBB/2006/69141

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

Yuchun Guo,¹Gabriel S. Eichler,^2,3Ying Feng,¹Donald E. Ingber,¹and Sui Huang¹

Received02 Jun 2006

Revised14 Aug 2006

Accepted25 Aug 2006

Published01 Nov 2006

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.

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Copyright

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.

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