Genome analysis profiles

Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288. 

Ma, L, Zhao, H., Deng, X. W. Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development 2003, 330, 969-981. 

Pellegrini, M., E.M. Marcotte, M.J. Thompson, D. Eisenberg, and T.O. Yeates, Assigning protein functions by comparative genome analysis protein phylogenetic profiles. Proc Natl Acad Sci USA, 1999. 96(8) 4285-8. 

Coco S, Defferrari R, Scaruffi P et al. Genome analysis and gene expression profiling of neuroblastoma and ganglioneuroblastoma reveal differences between neuroblastic and Schwannian stromal cells. J Pathol 2005 207-346-357. 

J. Hammond and G. Spanswick, Biochem. Educ. 25, 109-111 (1997). A Demonstration of Genomic DNA Profiling by RAPD Analysis. ... 

The contribution of in silico models to vaccine development comprises algorithms for accelerated in silico identification of relevant protein candidates in silico design of novel immunogens with improved expression, safety, and immunogenicity profiles and in silico design of nucleic acid-based, vectored, or live attenuated vaccines. In small molecule development, in silico models play a major role in comparative genomics, whole genome analysis,... 

Acad. Sci. V.S.A., 96, 4285 (1999). Assigning Protein Functions by Comparative Genome Analysis Protein Phylogenetic Profiles. 

Recent advances in micro-manipulation and hybridization, fluorescence labeling, and large-scale sequencing projects have led to new methods of expression profiling and genome analysis, loosely termed microarray analysis. This is an oblique description for a number of methods that utilize hybridization of labeled complex RNA probes to immobilized nucleotides arrayed at high density on a solid substrate to provide quantifiable data on relative expression levels. 

The following example illustrates how functional occurrence profiles are used in comparative genome analysis. In this example, such a profile is used to examine the presence of a specific pathway (i.e., C02 fixation) in a set of selected organisms, namely in the archaeal class of Methanomicrobium archaea. These organisms can first be selected using IMG s phylogenetic-based Genome Browser as shown in Fig. 3 (i) and then saved in order to focus the analysis context as previously discussed. 

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