Help@CSB.DB: The Graphical Validation & Gene Information Page
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This validation query allows for dynamical validation on demand of discovered co-responses, graphical (bi-) plots as well as more demanding statistic algorithms, such as bootstrap and jack-knife analyses. All algorithms are implemented as R scripts, which can be invoked upon user selection and generate a PDF output. These files can be optionally saved by the user for further reference. Furthermore this additional tool supports the detection of outliers, which may be associated with technical errors of the transcript measurements or with biological variance.
To get information of your choice for the Graphical Validation & Gene Information Page use the links listed below.
The Graphical Validation & Gene Information Page can be accessed if you click on a particular coefficient values (e.g. blue marked correlation coefficient). After invokation you see the following page.
Here is a picture and a graphic based introduction into the functionality of the Graphical Validation & Gene Information Page.
The gene information section contains information about your gene of interest and a second gene according your selection. If you click on the links, which are marked blue, you enter external, expert databases which provide further information for your selected gene.
Moreover you can get graphs for the two selected genes as well as validate the correlation with more sophisticated methods like bootstrap. The available methods can be accessed if you click on 'Expand All Methos' or if you click on a sub-category, like Scatterplot with confidence ellipse. If you press submit you get the default methods, which means a scatterplot with confidence ellipse (method: zoom-in region).
The 'Matrix Region' method produces a scatterplot in range of the minimum and maximum of log base 2 transformed expression measurements. The area boradered with dashed line represent the area where 95% of the expression measurement of the coresponding matrix were located. The minor and principal axis are plotted (see bottom graph). The principal axis represent the gene with higher variance. Moreover the 95% univariate ellipse is plotted.
The 'Zoom-In Region' method produces a scatterplot in range of the minimum and maximum of log base 2 transformed expression measurements for the two selected genes. The minor and principal axis are plotted (see bottom graph). The principal axis represent the gene with higher variance. Moreover the 95% confidence ellipse is plotted, which represent the area where the bivariate mean of gene X and Y are located with a probability of 95%.
Help: Matrices - Gene Co-Response Analyses). According to the detected outliers the correlation is re-computed (graph: bottom, right). Method B (blue colored) based on the robust Mahalanobis distance. The center (blue colored) is computed based on the 'mve' algorithm which is an robust procedure to estimate the mean and the covariance base on minimal ellipse (Rousseeuw & Leroy, 1987). Outliers defined by this method are labeled blue (and includes the black ones) and marked with the co-responding CSB.DB experiment id (see Help: Matrices - Gene Co-Response Analyses). According to the detected outliers the correlation is re-computed (graph: bottom, left).