Large-scale analysis

Washburn, M.P., Wolters, D., Yates, J.R., 3rd (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247. 

Kittler JF et al. Large-scale analysis of gene expression changes during acute and chronic delta9-THC in rats. Physiol Genomics 2000 3 175-185. 

Nobuhiro Takahashi and Toshiaki Isobe Proteomic Biology Using LC-MS Large Scale Analysis of Cellular Dynamics and Function... 

Nolan J, Mandy F (2006) Multiplexed and microparticle-based analyses. Quantitative tools for the large-scale analysis of biological systems. Cytometry A 69 318-325... 

Burns, N., Grimwade, B., Ross-Macdonald, P., Choi, E.-Y., Finberg, K., Roeder, G., and Snyder, M. (1994). Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8, 1087—1105. 

Despite these problems EST databases are a valuable source of large-scale analysis of human variation. They will become even more valuable as the data continue to grow at the present rate. An algorithm for computer-aided SNP mining should contain filters to eliminate the potential sequence errors. Such filters can be based on the probabilistic analysis of sequence features. It can also take into account that multiple occurrences of a variant are more trustworthy, and it may furthermore focus on improving the quality of base-calling if the fluorescent traces are available for closer srcutiny. 

Murakami Y, Saigo K, Takashima H, Minami M, Okanoue T, Brechot C et al (2005). Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Guf 54 1162-1168. 

In a more modified approach, differential display proteomics can also be done with no separation of proteins. This is called the protein chip approach. In this method, a variety of bait proteins such as antibodies, peptides, or protein fragments may be immobilized in an array format on specially treated surfaces. The surface is then probed with the samples of interest. Proteins that bind to the relevant target can then be analyzed by direct MALDI readout of the bound material (Nelson, 1997 Davies et ah, 1999). Lor example, well-characterized antibodies can be used as bait. Protein samples from two different cell states are then labeled by different fluorophores, mixed together, and used as probe. In such a case, the fluorescent color acts as an indicator for any change in the abundance of the protein that remains bound to the chip (Lueking et ah, 1999). A number of technical problems would still need to be overcome before applying this technique for large-scale analysis of proteins. 

For large-scale analysis, this strategy has been further modified for use in the array method (Ito et al., 2000 Uetz et al., 2000 Walhout et al., 2000). Such analyses in Sachromyces cerevisiae and Caenorhabditis elegans have already reported many potential interactions that need to be confirmed by further biological experimentation. Finally, another modification of the yeast two-hybrid system has been recently reported, termed reverse two-hybrid (Vidal and Endoh, 1999). This technique is being used to identify compounds and peptides that can disrupt protein-protein interactions and thus have an effect on various signaling pathways. 

ASAMIZU, E NAKAMURA, Y SATO, S., TABATA, S., A large scale analysis of cDNA in Arabidopsis thaliana Generation of 12,028 non-redundant expressed... 

Automated ultra-thin-layer gel electrophoresis was applied for large-scale analysis of SDS-protein complexes and for molecular-mass estimation of the proteins in the sample [12], Figure 13 compares the separations of two differ-... 

There are two major approaches to the large-scale analysis of subcellular location. One involves prediction of subcellular location based on protein sequence. The other involves experimental determination of the locations of proteins. 

Another description of large scale analysis come from AstraZeneca in a study directed towards the synthesis of a neurokinin inhibitor of the central nervous system [100]. The synthesis inherited from the research stage already contained a Newman-Kwart rearrangement for the introduction of the sulfur atom (Scheme 40). This step was maintained in the reaction scale-up [101,102]. 

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