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geNorm

 

geNorm is an algorithm that selects an optimal pair of reference genes out of a larger set of candidate genes. It calculates and compares the so called M-value of all candidate genes, eliminate the gene with highest M-value, and repeats the process until there is only two genes left. An M-value describes the variation of a gene compared to all other candidate genes. The last pair of candidates remaining is recommended as the optimum pair of reference genes (Vandesompele et al. (2002), Genome Biology 3 0034.1-0034.11). It is assumed that the candidate genes are not co-regulated. 

 

Open the Ref Gene tab among the analyses tabs in the top of the main window, and press the geNorm button to load the analysis into the Control panel. You need at least two genes to run the analysis, and at least three to give non-trivial results. Also, the data cannot contain any negative values, so make sure that it is not mean centered or autoscaled. 

 

    

 

    

 

geNorm is applied on copy number data or a quantity proportional copy numbers. If the data consists of Cq values, fold changes, or other logarithmic values, make sure that the Antilog2 check box is ticked, and GenEx will convert the data to linear scale only for the geNorm analysis. By default the check box is ticked, so remember to remove the tick if the data is already on linear scale. The result is summarized in the Control panel where you can see the optimal reference gene pair, as well as their M-value. The result is also presented as a table of each gene's M-value, and as a bar plot where the M-values are plotted and the recommended genes are indicated in red. The tabel can be sorted either by gene name or M-value. Click the column labels to switch between the two. 

 

    

 

    

 

Watch the tutorial Find reference genes from one group on how to select optimum reference genes from one sample group, and the tutorial Find reference genes for multiple groups on how to select optimum reference genes from grouped samples. To learn more about geNorm, visit http://medgen.ugent.be/~jvdesomp/genorm/.