By Eliot H. Ohlstein, Anthony G. Johnson, John D. Elliott (auth.), Richard S. Larson (eds.)

Includes absolutely up-to-date protocols at the state of the art of the fields progress
Provides step by step element crucial fro reproducible results
Contains key notes and implementation suggestion from the specialists

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This experiment has a simple experimental design (Fig. 2A). Nevertheless, it is important to predict what types of results are expected in order to design the appropriate filters. 2. Filter on Flags The first criterion is that only those genes that can actually be detected above background levels should be considered for further analysis. If a gene is expressed at such low levels that it cannot be distinguished from background in any of the samples, there is no sense in applying a filter to see whether its expression has increased.

A. (2004) Positive and negative determinants of target gene specificity in Myb transcription factors. J. Biol. Chem. 279, 29,519–29,527. 6. Rushton, J. , Davis, L. , and Ness, S. A. (2003) Distinct changes in gene expression induced by A-Myb, B-Myb and c-Myb proteins. Oncogene 22, 308–313. 7. Ferrando, A. , Neuberg, D. , et al. (2002) Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 1, 75–87. 8. , and Sausville, E. A. (2003) Genotoxic profiling of MCF-7 breast cancer cell line elucidates gene expression modifications underlying toxicity of the anticancer drug 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole.

For details). Generalized matrix inversion of the lead matrix was achieved with the singular value decomposition (SVD) routine implemented in Matlab. Entries in the diagonal matrix E were examined and entries with very small values (typically <10−2) were set to 0. Entries in the E−1 matrix were calculated by inverting each of the nonzero diagonal entries in the E matrix and leaving others as zero. The computation time is within minutes with a data set of about 6000 genes and 20 time points at a 16-CPU supercomputer running an IRIX operating system.

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