Bioinformatics and Drug Discovery by Eliot H. Ohlstein, Anthony G. Johnson, John D. Elliott

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 aspect crucial fro reproducible results
Contains key notes and implementation recommendation from the specialists

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However, if the researchers failed to balance the cohorts, they may have been misled. Because 80% of the original samples had good prognosis, a random selection of any sample would have an 80% chance of being in the good prognosis group. If the microarray analysis fails to perform better than random chance, it has not really worked. A better design would be to choose a balanced cohort, 50% with good and 50% with poor prognosis, to use as the training set. In this type of experiment, it is essential to get help from a qualified biostatistician before beginning, in order to obtain results that are valid and meaningful.

Before one moves to more complicated models, it is important to establish where the simple models fail. This is especially true when dealing with limited data with large statistical errors, as found in most microarray studies. Second, the linear model may act as a first approximation to a more complicated nonlinear expression. Any nonlinear function can be “linearized” through a power series expansion, and the linear model can be considered the first term in such an expansion. At this stage of sophistication and data quality, we are primarily seeking phenomenological connections, rather than quantitative mathematical connections.

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.

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