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J. Biol. Chem., Vol. 279, Issue 17, 17905-17913, April 23, 2004

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Pearson Correlation Analysis of Microarray Data Allows for the Identification of Genetic Targets for Early B-cell Factor^*

Robert Månsson, Panagiotis Tsapogas, Mikael Åkerlund, Anna Lagergren, Ramiro Gisler, and Mikael Sigvardsson

From the Department of Heamatopoetic Stemcell Biology, Stemcell Center, Lund University, S221 84 Lund, Sweden

B lymphocyte development is a complex biological process critically dependent on the transcription factor early B cell factor (EBF). To deepen understanding of the roles for EBF in this process, we have used Pearson correlation analysis to evaluate microarray data from a set of mouse B lymphoid cell lines representing different stages of development. Comparing the expression pattern of EBF to that of the other genes in the data set revealed that VpreB1, mb-1, and 5, all known target genes, presented high correlation values to EBF. High correlations were also seen for the VpreB3 and CD19 genes and biochemical as well as functional data supported that they are target genes for EBF even though the expression of CD19 was critically dependent of Pax-5. We also obtained evidence for extensive collaborative actions of EBF and E47 even though microarray analysis of hematopoetic progenitor cells ectopically expressing these proteins suggested that they activated only a subset of pre-B cell restricted genes.

Received for publication, January 20, 2004

^* This work was supported by the Swedish Medical Research Council (VRM), Cancerfonden, Crafoords Foundation, Kocks Foundation, Österlunds Foundation, and Barncancer fonden. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains the Appendix.

To whom correspondence should be addressed: BMC B12, S-221 84 Lund, Sweden. Tel.: 46-0-46-2223829; Fax: 46-0-46-2223600; E-mail: mikael.sigvardsson{at}stemcell.lu.se.

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