Figure 9
From: Inferring interaction type in gene regulatory networks using co-expression data
Deciphering interaction type from co-expression patterns. a, b The two-dimensional grids are constructed for two selected gene pairs with known activating or inhibitory effect on each other. The color density for each cell in the grid represents the computed PMI for that cell multiplied in the occurrence probability of the cell and corresponding rescaling value (determined based on the rescaling matrix). The PMI and occurrence probability is calculated based on the associated transcriptome data. Red indicates positive score and blue represents negative score (defined based on the M3 rescaling matrix). SIREN score is determined by summing up the calculated values for each combination of bins. a For two example genes with known activating relationships (JUN and ATF3), cells defined as activating have non-zero values and cells defined as inhibitory relationship, have zero values. b This situation is reversed for two genes with known inhibitory relationship (ZEB1 and CDH1).