A large-scale comparison of microarray platforms published in Nature Biotechnology
The bioinformatics effort at the Norwegian Radium Hospital has recently published a comparison of microarray platforms as a research article in Nature Biotechnology (impact factor 22.738). The bulk of the bioinformatics analysis in this paper has been performed by Fang Liu (photo) from Eivind Hovig's group at the Department of Tumor Biology. The paper is a part of her doctoral thesis, and she thus shares the first authorship.
This is one result of a collaboration between scientists at Harvard and Oslo, and it is expected that further papers will follow, as more microarray platforms and other profiling technologies will be examined using the same framework.
This is one result of a collaboration between scientists at Harvard and Oslo, and it is expected that further papers will follow, as more microarray platforms and other profiling technologies will be examined using the same framework.
The main finding is that modern RNA profiling platforms are relatively robust and report relatively consistent on genes being of high and intermediate expression values. The concordance between platforms increase further when the probe sequence is matched to the same exon.
Links:
Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006 Jul 2; (Link to PubMed)
Link to fulltext version from publishers site (www.nature.com)
The web pages of Eivind Hovig's group - radium.no/hovig - Metastasis: molecular studies and development of methods
Fang Liu
Department of Tumor Biology
Institute for Cancer Research
Links:
Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006 Jul 2; (Link to PubMed)
Link to fulltext version from publishers site (www.nature.com)
The web pages of Eivind Hovig's group - radium.no/hovig - Metastasis: molecular studies and development of methods
Fang Liu
Department of Tumor Biology
Institute for Cancer Research