Estimating the Number of Replicates

In this section we provide a simplified method that provides a rough estimate of the number of replicates required for a parametric test, such as ANOVA or t test (van Belle 2002). The assumptions and limitations of the method are discussed. A spreadsheet program is sufficient for these calculations. To estimate the number of replicates in a microarray study we must define the following the desired magnitude of change in expression level, the expected variance of signal for the probeset of...

Tracksystems

Chip Design Which genes probes clones LIMS Chip Construction Chip layout, printing AIMS Data Acquisition RNA extraction, labeling, hyb, Image capture LIMS ImageAnalysis Convert scanned Image to expression leve Is AIMS Data Analysis Normalization, filtering, clustering, Software classification, pattern discovery, biological interpretation Fig. 10.7 Microarray experimental components - information management (IM) systems for data acquisition and biological interpretation. cal and experimental...

Detection of Protein Modifications by MS and MSMS

In this section some aspects of protein modification analysis, i. e., characterization of isolated proteins, are discussed. Figure 6.9 provides a visual display of the MS and MS MS dimensions of a protein digest analysis. In front, the survey MS spectrum of a protein digest is displayed. Orthogonal to this survey spectrum is the MS MS dimension, with a single MS MS spectrum given as example. The sequence- and modification-specificity of the MS approach is located in the MS MS dimension, since...

Brief Survey of Promoterrecognition Programs

Two different approaches have been applied so far to promoter recognition. The first approach is purely sequence-based, making use of different statistics of nucleotides and oligonucleotides in the promoter sequences without considering known promoter signals and cis-elements. Specific features of the distribution of nucleotides and oligonucleotides of different lengths (di-, tri-, and longer oligonucleotides) are revealed in the training set of known promoters, and these features are then used...

DNA Mapping SNP Arrays

Due to the high frequency of polymorphisms in drug susceptibility genes, it is likely that more than one gene will be involved in most instances of inherited adverse drug reactions (Garte 2001). Whole genome single nucleotide polymorphism (SNP) profiling is an unbiased method of determining genetic predisposing factors for adverse drug responses (Pirmohamed and Park 2001). Once a polymorphic region is found, resequencing arrays can determine the exact sequences in that region. Until now these...

Challenges for the Future

Future development of mammalian DNA microarrays representing a major portion of intergenic regions would be a great advancement in the genome-wide location analysis of potential targets by 'ChIP on a chip'. Researchers have looked for various types of signals around the transcriptional start site to improve promoter prediction 75 . The RNA polymerase II core promoters can be classified into two main classes, one associated with CpG islands and the other not. The first class corresponds to the...

Forensic and Chemical Warfare Toxicology

NMR is not widely used in forensic toxicology, probably due to the perceived poor sensitivity and the lack of routine access to high-field (> 500 MHz) NMR instrumentation. Some interesting historical examples using low-field magnets demonstrate the versatility of NMR for identifying biomarkers of poisoning. Cartigny and colleagues 36 reported on a 4-month-old girl who presented with agitation, fever, dehydration, and metabolic acidosis. Metabolites including o-hydroxyhippuric acid,...

Protein Modifications and Their MSMS Reactions

So far, > 100 covalent modifications of proteins have been described e.g., 20-22 . The annotated protein database SwissProt 23 is a rich source of well established covalent protein modifications. Many covalent modifications are accompanied by an increase in molecular weight and an increase in acidity (lower pi value), including deamidation, phosphorylation, sulfation, N-acylation, and cysteic acid formation. A selection of covalent modifications is given in Table 6.1, together with...

Conventional NMR Spectroscopy

Solution state NMR spectroscopy is the study of molecules by recording the interaction of radiofrequency electromagnetic radiation with the nuclei of molecules in solution when placed in a strong magnetic field. The circulation of electrons around nuclei in different electronic environments creates local magnetic environments. These local magnetic fields give rise to characteristic chemical shifts suitable for functional group identification. Moreover, the presence of coupling between pairs of...