DNA Microarrays and Gene Expression: From Experiments to by Pierre Baldi

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By Pierre Baldi

Substantial facts acquisition technologies--such as genome sequencing, high-throughput drug screening, and DNA arrays--are within the strategy of revolutionizing biology and drugs. This concise, easy and interdisciplinary advisor to DNA microarray know-how is an creation and a reference for either biologists and computational scientists. The authors describe the underlying applied sciences and supply an understanding of the "noise" and pitfalls found in the knowledge generated. in addition they supply an idea of the several info mining innovations and algorithms which are to be had to interpret facts, and the benefits and drawbacks of every in differing occasions.

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Extra info for DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling

Example text

Next, the Lrp structural gene was deleted from this strain to produce the otherwise isogenic strain (IH-G2491; ilvPG::lacZYA, lrpϪ) [5]. The ability to control this source of biological variation in a model organism such as E. coli with an easily manipulated genetic system is an obvious advantage for gene expression profiling experiments. However, most systems are not as easily controlled. For example, human samples obtained from biopsy materials will not only differ in genotype but also in cell types.

The laser beam enters from above and is reflected by the beam splitter (a dichroic or multichroic filter that reflects light of short wavelengths and transmits light of longer wavelengths). The laser beam is focused to a spot on the surface of the glass slide by an objective lens and excites fluorophores in the focal plane of the objective. The fluorescent emissions (and the reflected laser beam rays) are collected by the objective and collimated into parallel rays (solid lines). Most of the reflected laser rays (Ͼ95%) are reflected back toward the laser source by the beam splitter.

Another set of filters (Filter 3 and Filter 4) was used for Experiments 3 and 4 as described for Experiments 1 and 2. This protocol results in duplicate filter data for four experiments performed with the cDNA probes complementary to four independently prepared cDNA probe sets. Thus, since each filter contains duplicate spots for each ORF and duplicate filters are hydridized for each experiment, four measurements for each ORF are obtained from each of four experiments. Gene expression profiling in bacteria 35 operon (ORFs in the same mRNA transcript) were detected, others were not.

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