Transcriptome information

The use of new transcriptome information for discovery of novel drug candidates is desirable, as the control of schistosomiasis relies mostly on the use of a single drug, praziquantel, a heterocyclic pyrazino-isoquinolone. This drug exerts multiple effects, such as damage to the tegumental membrane, changes in calcium flux and muscular contractions in the parasite by a mechanism or mechanisms that are not... 

Therefore, it is assumed that in near future it will become possible to diagnose the probability of asthma or other diseases of allergic origin, e.g., food allergies, in appropriately equipped clinical laboratories, also by means of screening all SNP and transcriptome information related to the diseases. Nowadays, however, despite extensive research, even the most risky SNP combination related to asthma has only a twofold odds ratio with controls and most SNP research papers deal only with statistical probability (Saito et al., 2003). 

Similarly, we have described how information related to protein-splicing variants, amino acid peptide variants (polymorphisms), and PTMs is being introduced in data analysis pipelines in order to increase the rate of identifiable peptides. The introduction of genomics and transcriptomics information, often neglected in routine proteomics analyses, will enable the characterization of myriad splicing variants and amino acid polymorphisms, as well as the development of robust proteomics analysis pipelines, which will contribute to elucidate their role in health and disease states. These tools will make it possible to uncover a new layer of the proteome complexity and to expand the information available from cellular systems and the potential implication of these protein variants in different physiological processes. Finally, several bioinformatics tools that perform unbiased PTM analysis have also been reviewed. The tools that are currently being developed and refined tackle... 

In contrast to the large quantity of genome and transcriptome information available for model plants on a variety of websites (A. thaliana (http //arabidopsis.org), O. sativa (http //rice. plantbiology.msu.edu http //rapdb.dna.affrc. go.jp) and others), genome information is not yet available for most medicinal plants. Conse-... 

Additionally, the cellular location at which the resultant polypeptide will function often cannot be predicted from RNA detection/sequences nor can detailed information regarding how the polypeptide product s functional activity will be regulated (e.g. via post-translational mechanisms such as phosphorylation, partial proteolysis, etc.). Therefore, protein-based drug leads/targets are often more successfully identified by direct examination of the expressed protein complement of the cell, i.e. its proteome. Like the transcriptome (total cellular RNA content) and in contrast to the genome, the proteome is not static with changes in cellular... 

The EST has continued to be a popular test subject to further optimization, especially through the addition of alternative pathways of differentiation and the addition of molecular markers of effects. Besides cardiac muscle differentiation, other cell types such as neurons (29-31), osteoblasts (32), adipocytes (33), and hepato-cytes (34) have been generated in dedicated differentiation protocols, providing additional opportunities for testing the interference of differentiation pathways with chemical exposures. The addition of transcriptomics approaches to measure differential gene expression, both as influenced by the differentiation process as well as due to chemical exposure, has proven informative and may enhance the predictability of EST assays (35). The extension of this concept to human embryonic stem cell lines is still in its infancy, but has opened a new realm of options that bypasses the need for interspecies extrapolation (36). 

The information gleaned from analysis of the genome, transcriptome and proteome can be integrated to prioritize proteins for intensive investigation. Each will need to be expressed as a recombinant or formulated as a DNA construct for rigorous testing of its protective... 

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