Figure 3

Comparison between gene expression (mRNA) levels calculated by NCA and (previously) measured by microarray analysis. From measured gene expression values (matrix [log₁₀G]) across four cell types (conditions), NCA deduced the unknown TF activities (matrix [log₁₀TFA]) and the TF-gene CS (matrix [CS]) in Eq. {1} for seven NCA-compliant TFs. Based on this, the gene expression values simulated by NCA were calculated as the product of the TF-gene CS (matrix [CS]), and the TF activities (matrix [log₁₀TFA]). This plot compares the NCA simulated gene expression values with experimental gene expression levels for the four cell types. A good match was seen between both (R² = 0.816) depicting the ability of NCA model to account for the gene expression measurements. The horizontal error bars are from replicates for the measured gene expression across all 4 cell types, the vertical error bars are from the corresponding replicates of NCA simulated gene expression values.