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BIOINFORMATICS

Finding Unexpected Patterns in Microarray Data¹

IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, 1417-Buenos Aires, Argentina (S.P., J.J.C.); Instituto de Investigaciones en Ingenieria Genetica y Biologia Molecular, Vuelta de Obligado 2490, 1428-Buenos Aires, Argentina (M.A.M., J.M.); and Syngenta Biotechnology, Inc., 3054 Cornwallis Road, Research Triangle Park, North Carolina 27709 (T.Z.)

We describe the performance of a protocol based on the sequential application of unsupervised and supervised methods to analyze microarray samples defined by a combination of factors. Correspondence analysis is used to visualize the emerging patterns of three set of novel or previously published data: photoreceptor mutants of Arabidopsis grown under different light/dark conditions, Arabidopsis exposed to different types of biotic and abiotic stress, and human acute leukemia. We find, for instance, that light has a dramatic effect on plants despite the absence of the four major photoreceptors, that bacterial-, fungal-, and viral-induced responses converge at later stages of attack, and that sample preparation procedures used in different hospitals have large effects on transcriptome patterns. We use canonical discriminant analysis to identify the genes associated with these patters and hierarchical clustering to find groups of coregulated genes that are easily visualized in a second round of correspondence analysis and ordered tables. The unconventional combination of standard descriptive multivariate methods offers a previously unrecognized tool to uncover unexpected information.

¹ This work was supported by Fondo Nacional de Ciencia y Técnica (grant no. PICT 06739 to J.J.C.), by the University of Buenos Aires (grant no. G 067 to J.J.C.), by the National Research Council of Argentina (Consejo Nacional de Investigaciones Científicas y Técnicas grant no. PID 888 to J.J.C.), and by Fundación Antorchas (grant no. 14116-16 to J.J.C.).

^* Corresponding author; e-mail casal{at}ifeva.edu.ar; fax 5411-4514-8730.

Received June 17, 2003; returned for revision July 23, 2003; accepted August 31, 2003.

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