Vector algebra in the analysis of genome-wide expression data 英文参考文献.docVIP

/2002/3/3/research/0011.1 Research Vector algebra in the analysis of genome-wide expression data
inny G Kuruvilla*, Peter J Park? and Stuart L Schreiber* Addresses: *Howard Hughes Medical Institute, Bauer Center for Genomics Research, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. ?Department of Biostatistics, Harvard School of Public Health, Informatics Program, Children?s Hospital, Harvard Medical School, Boston, MA 02115, USA. Correspondence: Stuart L Schreiber. E-mail: sls@ Published: 13 February 2002 Received: 20 August 2001 Revised: 14 December 2001 Accepted: 11 January 2002 GenomeBiology 2002, 3(3):research0011.1–0011.11 The electronic version of this article is the complete one and can be found online at /2002/3/3/research/0011 ? 2002 Kuruvilla et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Data from thousands of transcription-profiling experiments in organisms ranging from yeast to humans are now publicly available. How best to analyze these data remains an important challenge. A variety of tools have been used for this purpose, including hierarchical clustering, self-organizing maps and principal components analysis. In particular, concepts from vector algebra have proven useful in the study of genome-wide expression data. Results: Here we present a framework based on vector algebra for the analysis of transcription profiles that is geometrically intuitive and computationally efficient. Concepts in vector algebra such as angles, magnitudes, subspaces, singular value decomposition, bases and projections have natural and powerful interpretations in the analysis of microarray data. Angles in particular offer a rigorous method of defining ‘similarity’ and are useful in evaluating the claims of a microarray-based study. We present a sample analysis of cells treated with rapamycin, an immunosuppressant who