Fig. 3

Retrieving the chromatin signature of the H1-specific enhancers. Three examples of enhancers are shown in Parts a–c. A row in one of these plots represents the distribution of one mark around a region; red (blue) color indicates the presence (absence) of a mark. It is hard to see a common pattern in these three examples. The signature learned by the Hebbian network is captured by the HebbPlot shown in Part d. A row in the HebbPlot represents the distribution of a mark around all enhancers in the data set. The closer the color to red, the higher the certainty of the presence of a mark around the corresponding sub-region. The HebbPlot is characterized by four zones. The top most zone represents chromatin marks that are absent from the enhancer regions, whereas the next three zones represent the present marks with increasing certainty. A conventional plot of the intensities of all marks around every region in the data set in shown in Part e. Many marks show depressions near the center of the plot; however, some peaks are mixed with these depressions in the conventional plot. In contrast, these depressions correspond to the ellipse in the middle of the third zone of the HebbPlot. This ellipse is very clear. Further, marks of similar intensities obstruct one another in the conventional plot. This is not the case with HebbPlot because every mark is represented by a separate row. An average plot is displayed in Part f. This plot shows a similar — but fuzzy — pattern to the one found by the network