Transcriptomics, Proteomics, and Metabolomics

Integrated Functional Genomics Transcriptomics, Proteomics, and Metabolomics... 

This rather recently acquired ability to generate transcriptomic, proteomic, and metabolomic data in almost intimidating quantities has far-reaching impact on all biological sciences and already shapes the face of most of the current molecular biology. However, paraphrasing Poincare, a mere accumulation of data and disconnected facts is no more knowledge than a heap of stones is a house. Concomitant to the development of novel experimental methods,... 

Characterizing the metabolome is only one component which needs to be integrated with its counterparts to realize its potential contributions to drug discovery and development. When all of the work has been done to define the universe of the transcriptome, proteome, and metabolome, and biomarker sets have been identified, 90% of the work remains in the validation and acceptance of these patterns. 

It is already well known that bioactive food compounds can interact with genes affecting transcription factors, protein expression, and metabolite production. The study of these complex interactions requires the development of advanced analytical approaches combined with bioinformatics. Thus, to carry out these studies transcriptomics, proteomics, and metabolomics approaches are now being employed together with an adequate integration of the information that... 

Figure 1 The physiological state of the cell is measured at several levels in a functional genomic approach, all of which interact with one another to form a highly interconnected network. In particular, differences in the transcriptome, proteome, and metabolome are monitored as a means to study gene function and cellular responses to external stimuli.

These new omics technologies will also enable us to efficiently identify novel compounds of value to both the Agrochemical and Pharmaceutical industries. It is of crucial importance that the data that results from high throughput analyses of the genome, transcriptome, proteome and metabolome of crop plants and foeir relatives is archived in an appropriately structured and indexed manner. This will enable it to be fully integrated and data-mined over an extensive period as our ability to formulate increasingly sophisticated queries on these data sets develops. 

Understanding complex living systems or supersystems on a molecular level needs comprehensive data analysis, collection, and mining strategies. Today s Omics technologies, such as transcriptomics, proteomics, and metabolomics,... 

One last interesting point should be drawn to the combination of transcriptomics, proteomics, and metabolomics. Proteomics and metabolomics are both based on similar chemical analysis techniques LC-MS. It might be possible that in the future new work based on the combination of both or all three will be published. Virtually, high-resolution instruments such as the latest... 

Wilmes A et al (2013) Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress. J Proteomics 79 180-194... 

Many existing chemicals have not been thoroughly evaluated for potential developmental/adult neurotoxicity. Currently there is a need for cost-effective predictive tools and testing methods to generate human safety information to make regulatory decisions. The application of innovative methods such as high content OMICS techniques (transcriptomics, proteomics, and metabolomics) (described in Chap. 18) in combination with stable human in vitro... 

The use of human-derived stable differentiated cultures of target organs will be extremely useful for the discovery and development of new translational biomarkers. Omic technologies such as transcriptomics, proteomics, and metabolomics have proven to be excellent tools for understanding drug-induced perturbations, especially when used in combination with appropriate cell culture models [13, 122], The further understanding of how cells differentiate and maintain tissue-specific functions will also be crucial for the discovery of new biomarkers [123]. Importantly, the development of new mechanistically informative biomarkers is not just useful for clinical applications, but these markers will also be useful to drive the development of better, more predictive, human-based in vitro test systems to improve on the predictive power of whole-animal experiments in preclinical testing scenarios. 

Heijne W H, Kienhuis A S, van Ommen B, et al. (2005). Systems toxicology Applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology. Expert Rev. Proteomics. 2 767-780. 

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