Differential expression profiles

Lu, Z., Hu, L., Evers, S., Chen, J., Shen, Y. (2004). Differential expression profiling of human pancreatic adenocarcinoma and healthy pancreatic tissue. Proteomics 4, 3975-3988. 

Alterations in the protein pattern are immanent for mammalian body fluids or tissues. Differential expression profiles for the comparison of distinct samples are to be expected due to the biological variability related to patient age, gender or lifestyle. In order to distinguish disease-related features from false-positive differences the critical validation and assessment of putative markers is of fundamental importance (Zolg and Langen, 2004). 

Niedemberg A, Scherer CR, Busch AE, Kostenis E (2002) Comparative analysis of human and rat S1P(5) (edg8) differential expression profiles and sensitivities to antagonists. Biochem Pharmacol 64 1243— 1250... 

Probe selection is dependent on the experimental design, and in the classic examples of differential expression profiling may include comparisons of nucleic acids based on pre- and postreatment of cells, animals, or tissues different disease states different tissues or cell types and subcellular localization. The number and type of comparison determine the complexity of data produced. The simplest experiment would involve the direct comparison of two nucleic acid samples which, depending on the complexity of the samples compared, may provide a few or many hundreds of differences. This highlights an important aspect of experimental design. Heterogeneous tissues provide a source of variability that is difficult to control for, and use of such tissues should be carefully considered. 

Conesa, A. Nueda, M. Ferrer, A. Talon M. (2006). maSigPro a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics, Vol. 22, pp. 1096-1102. 

Yang, H., A. Hui, G. Pampalakis et al. 2009. DirecL electronic microRNA detection for the rapid determination of differential expression profiles. Angew. Chem. Int. Ed 48 8561-8564. 

Fig. 14.1. The Thl/Th2 balance is central to the regulation of normal wound repair. Tissue injury results in the initiation of an inflammatory response, mediated by a variety of cells and their by-products. Immune cells are recruited and cross-regulate the Thl/ Th2 balance that occurs in response to the cytokine environment. This balance is in turn cross-regulated by the chemokine/chemokine-receptor expression profile, which functions to amplify the inflammatory process. Cells residing in the injured tissue release profibrotic mediators, which promote fibroblast activation, proliferation, and differentiation to the myofibroblast phenotype. Myofibroblasts produce collagen to repair damaged tissue, which is an event that is favored by the inhibition of MMP activity. The Thl/Th2 balance is central to whether a normal or aberrant wound-repair process is established A Thl environment promotes normal tissue resolution (fibrinolysis), whereas a Th2 environment maintains the progression of fibrotic disease (excessive collagen deposition).

For these reasons we have developed a different approach that measures differential expression of intact proteins.21 In this approach the proteins are extracted from the cell, separated on an HPLC column, ionized via electrospray, and automatically deconvoluted into their respective uncharged nominal masses. By this methodology it is then possible to obtain accurate, intact protein profiles of the individual strains of bacteria. Because the masses of the detected proteins are accurate to +2 Da from run to run, it is possible to subtract protein profiles from known strains to quickly identify differences in protein expression among newly mutated strains. 

O Differential effects of compounds - in vivo or in vitro - on gene expression, among the entirety of expressed genes O Assessed by expression profiling O A tool for compound selection/drug discovery... 

Biochips can be used for either measuring differential expression between two populations or for testing for the presence of a DNA sequence (resequencing). Protein chips have been applied in expression profiling and antibody detection, binding specificities of a protein expression library and protein-protein interactions. 

FIGURE 15.3 Outline of experimental protocol used for ICAT differential protein expression profiling. Protein mixtures from two cell populations are labeled with light or heavy isotopic versions of a cleavable ICAT reagent. Labeled proteins are combined, subject to multidimensional separation by SCX, RP, and avidin affinity chromatography, then analyzed by tandem MS for peptide and protein identification. Based on the relative ratio of the two isotopically labeled peptides, a relative abundance of protein expression can be determined. 

The choriocarcinoma cell line JAr bears close resemblance to early trophoblast, as their secretion pattern of hCG and steroids is similar, and the cells can differentiate into syncytiotrophoblasts in vitro [71], In a study comparing efflux transporter expression and activity in trophoblast cell lines and choriocarcinoma cells, the expression profiles indicated that while BeWo are more... 

Matz M, Usman N, Shagin D, Bogdanova E, Lukyanov S. 1997. Ordered differential display a simple method for systematic comparison of gene expression profiles. Nucleic... 

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