Q:
I am reading your paper "Classification of human genomic regions basedon experimentally determined binding sites of more than 100 transcription-related factors" and I have some questions.
In figure 1 what do the colors mean?
I also couldn’t understand plots in figure 4. what are the black dots, the error bars and the black line ?
I would be grateful if you answer my questions.

A:
In figure one different colors are used for different types of regions. For each type of regions, one color is used as the background color as one color is used to show the signal level.

Figure four shows standard Box-and Whisker plots (http://en.wikipedia.org/wiki/Box_plot). The dots are the means of the distributions. The upper and lower lines are the non-outlier maximum and minimum values, respectively. The black lines in the middle are the medians.