Transcriptome profiling

Kiister H etal.. Development of bioinfo rmatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses, Phytochemistry 68 19—32, 2007. 

Jones DL, Petty J, Hoyle DC, Hayes A, Ragni E, Popolo L, Oliver SG, Stateva LI (2003) Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. Physiol Genomics 16 107-118... 

As it has been discussed in this chapter, transcriptomic profiling of food crops is a hot application for RNA-Seq technologies. Nevertheless, the applicability of RNA-Seq in Food Science and Nutrition is still in its infancy and it is not fully exploited yet. In the near future, it can be anticipated that many relevant topics in Food Science will benefit from RNA-Seq techniques. For instance in Nutrigenomics studies, it can be expected that RNA-Seq studies will improve our limited understanding of the roles of nutritional compounds... 

TABLE 1 Transcriptomics Profiling of GMOs Using Microarray Technique... 

Choi JH, Lee SJ, Lee SJ et al (2003) Enhanced production of insulin-like growth factor I fusion protein in Escherichia coli by coexpression of the down-regulated genes identified by transcriptome profiling. Appl Environ Microbiol 69 4737-4742... 

Scherl,A., Francois, P., Bento, M., Deshusses, J.M., Charbonnier, I., Converset, V., Huyghe, A., Walter,N., Hoogland, C., Appel, R.D., Sanchez, J.C., Zimmermann-Ivol, C.G., Corthals, G.L., Hochstrasser, D.F. and Schrenzel, J. (2005) Correlation of pro teomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth. J. Microbiol. Methods 60, 247-257. 

Dyhrman, S. T., Haley, S. T., Birkeland, S. R., Wurch, L. L., Cipriano, M. J., and McArthur, A. G. (2006). Long serial analysis of gene expression for gene discovery and transcriptome profiling in the widespread marine coccolithophore EmUiania huxleyi. Appl. Environ. Microbiol. 11, 252—260. 

Transcriptome profiling discovery of transcribed SNPs or somatic mutations (60)... 

Comprehensive transcriptome profiling studies using RNA-Seq (124) have found evidence for many novel exons, and the number of identified alternative splicing forms is much larger than previously expected (137). As alternatively spliced gene structures can be very different from the initial predicted gene structure, current ab initio and sequence similarity methods are not adequate to validate such predictions. Instead, mRNA sequences from RNA-Seq are translated to proteins and used as databases to identify the protein products of these novel exons, even though the final number of sequences that actually become functional proteins in vivo remains unknown (138,139). 

Roberts, G.C. and Hudson, A.P. 2006. Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling. Mol. Gen. Genomics 276,170-186. 

Prieto C et al (2008) Human gene coexpression landscape confident network derived from tissue transcriptomic profiles. PLoS One 3(12) e3911... 

Carapau, D., Kruhofer, M., Chatalbash, A., Orengo, J. M., Mota, M. M., and Rodriguez, A. (2007). Transcriptome profile of dendritic cells during malaria cAMP regulation of IL-6. Cell Microbiol. 9,1738-1752. 

Kaiser, K., Matuschewski, K., Camargo, N., Ross, J., and Kappe, S. H. (2004). Differential transcriptome profiling identifies Plasmodium genes encoding pre-erythrocytic stage-specific proteins. Mol. Microbiol. 51,1221-1232. 

Sadlier D M, Connolly S B, Kieran N E, et al. (2004). Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy. /. Biolog. Chem. 279 29670-29680. 

---