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The stereotypical use case of biclustering in bioinformatics is the analysis of co-expressed genes (with measured expression values) from a dataset under a (sub set of conditions.
The Normalized Shannon Entropy of a transcriptional sample profile is calculated associating the measured expression values of a gene with the relatively probability of being expressed.
Step 1 removes wells where no cells were loaded, and thus all measured expression values are null.
For each target gene we had 59 iterations, and we calculated the Pearson correlation coefficient (PCC) between the measured expression values and the predicted ones.
Log values are correlations for gene expression patterns that have undergone log2 transformation, and non-log values are determined straight from the measured expression values.
PCR was conducted with (i) different cycle numbers (25, 30 and 32) and (ii) different template cDNA concentrations to validate the linearity of the measured expression values.
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Microarray technology and other high-throughput methods are used to measure expression values of thousands of genes over different samples/experimental conditions.
With qBasePlus we measured expression stability (M values) and coefficients of variation (CV values).
Before analysis, a first filtering step removed from the dataset the genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples.
Before analysis, a filtering process removed the genes with low and poorly measured expression, as defined by an expression value inferior to 100 units in all breast cancer tissue and normal tissue samples, from the dataset.
For example, when the elements are genes, we may have measured differential expression values, as well as measured ChIP-Seq signals.
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compared expression values
estimated expression values
demonstrated expression values
calculated expression values
measured expression of
moderate expression values
measured expression levels
measured exposure values
measured expression changes
measured p values
measured force values
measured expression patterns
measured parameter values
measured expression profiles
mapped expression values
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