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Objective
The presented method was created to overcome the ambiguity and human intervention while creating the differential displays via aligning the 2D-PAGEs. Besides, if the conventional differential display reflects only the changes of the individual spots, the COVAG method is able to trace the changes of the spot ensembles, thus providing the insight into the protein networks. Method Conceptuality of COVAG resides by the standardized representation of the digital 2D gels (spot lists): spot list from each gel is self-organized. Produced map (SOM) encounters for all principal features of the underlying gel image. Important that SOM size and shape doesn't depend on the artificial aberrations of the source image. Next, a collection of SOMs is converted to the single array of node-dependent vectors (NDV). Each array's cell contains the information on how the particular SOM node varies throughout the whole collection of SOMs. By selecting the certain node on can proceed from the array of NDVs to the co-variance matrix (CovM). Elements of the CovM denote if there is the co-variance between the selected node and any other node. As if each node becomes the selected one in a turn, actually the series of node-dependent co-variance matrices appear. Finally, a series of CovM is projected onto the unified hyperplane by application of the Multi-Dimensional Scaling (MDS) method. At the hyperplane those spots appear together, which co-varied in the original gel images. Co-variation may come from the simultaneous changes in pI, masses or intensities of the sport that may occupy even the distant positions on the gels. Differential Display of Co-variations Assuming that there are control and experimental batches of 2D-PAGEs, the COVAG can produce the unified hyperplanes, and batch-specific hyperplanes. By comparing these three one can get the idea which co-variances contribute to the difference between control and experimental batches. Unraveling the Protein Networks Performing the cluster analysis of the hyperplane produced by COVAG one can get the lists of proteins (spots), which might be involved into the same metabolic processes within the cell. |