Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies 英文参考文献.docVIP

Open Access M d 2007NilssonetVoal.lumeetho8, Issue 5, Article R74 Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies Bj?rn Nilsson*, Petra H?kansson*?, Mikael Johansson?, Sven Nelander? and Thoas Fioretos* Addresses: *Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden. ?Department of Automatic Control, Royal Institute of Technology, SE-100 44 Stockholm, Sweden. ?Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. Correspondence: Bj?rn Nilsson. Email: bjorn.nilsson@med.lu.se Published: 8 May 2007 Received: 6 January 2007 Revised: 2 April 2007 Accepted: 8 May 2007 Genome Biology 2007, 8:R74 (doi:10.1186/gb-2007-8-5-r74) The electronic version of this article is the complete one and can be found online at /2007/8/5/R74 ? 2007 Nilsson et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. OntologicalanpdNsteawt sotnictgene-expressionaollloygpicoawlearnfually.si/spanalysismethods are described for microarray data interpretation that, unlike existing approaches, are threshold-free Abstract Ontological analysis facilitates the interpretation of microarray data. Here we describe new ontological analysis methods which, unlike existing approaches, are threshold-free and statistically powerful. We perform extensive evaluations and introduce a new concept, detection spectra, to characterize methods. We show that different ontological analysis methods exhibit distinct detection spectra, and that it is critical to account for this diversity. Our results argue strongly against the continued use of existing methods, and provide directions towards an enh