Skip Navigation


Bioinformatics Advance Access originally published online on July 15, 2004
Bioinformatics 2004 20(18):3431-3441; doi:10.1093/bioinformatics/bth421
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/18/3431    most recent
bth421v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Haverty, P. M.
Right arrow Articles by Weng, Z.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Haverty, P. M.
Right arrow Articles by Weng, Z.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Limited agreement among three global gene expression methods highlights the requirement for non-global validation

Peter M. Haverty 1, Li-Li Hsiao 2, Steven R. Gullans 2, Ulla Hansen 1,3 and Zhiping Weng 1,4,*

1 Bioinformatics Program, 2 Departments of Medicine and Neurology, Brigham and Women's Hospital, Harvard Medical School, 3 Department of Biology and 4 Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA

Received on December 14, 2003; revised on June 29, 2004; accepted on July 10, 2004
Advance Access Publication July 15, 2004

Motivation: DNA microarrays have revolutionized biological research, but their reliability and accuracy have not been extensively evaluated. Thorough testing of microarrays through comparison to dissimilar gene expression methods is necessary in order to determine their accuracy.

Results: We have systematically compared three global gene expression methods on all available histologically normal samples from five human organ types. The data included 25 Affymetrix high-density oligonucleotide array experiments, 23 expressed sequence tag based expression (EBE) experiments and 5 SAGE experiments. The reported gene-by-gene expression patterns showed a wide range of correlations between pairs of methods. This level of agreement was sufficient for accurate clustering of datasets from the same tissue and dissimilar methods, but highlights the need for thorough validation of individual gene expression measurements by alternate, non-global methods. Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels.

Contact: zhiping{at}bu.edu

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Plant Physiol.Home page
R. A.C. Mitchell, P. Dupree, and P. R. Shewry
A Novel Bioinformatics Approach Identifies Candidate Genes for the Synthesis and Feruloylation of Arabinoxylan
Plant Physiology, May 1, 2007; 144(1): 43 - 53.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Qian, N. Esumi, Y. Chen, Q. Wang, I. Chowers, and D. J. Zack
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation
Nucleic Acids Res., June 20, 2005; 33(11): 3479 - 3491.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
C. P. Denton, G. E. Lindahl, K. Khan, X. Shiwen, V. H. Ong, N. J. Gaspar, K. Lazaridis, D. R. Edwards, A. Leask, M. Eastwood, et al.
Activation of Key Profibrotic Mechanisms in Transgenic Fibroblasts Expressing Kinase-deficient Type II Transforming Growth Factor-{beta} Receptor (T{beta}RII{Delta}k)
J. Biol. Chem., April 22, 2005; 280(16): 16053 - 16065.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
J. Cai, D. Ash, L. E. Kotch, E. W. Jabs, T. Attie-Bitach, J. Auge, G. Mattei, H. Etchevers, M. Vekemans, Y. Korshunova, et al.
Gene expression in pharyngeal arch 1 during human embryonic development
Hum. Mol. Genet., April 1, 2005; 14(7): 903 - 912.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.