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Fig. 3 | BMC Bioinformatics

Fig. 3

From: The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data

Fig. 3

a An illustration of the CGP-based objective function Q: Q is maximum if ON genes and OFF genes are perfectly separated on the 3D genome; Q is close to zero if ON and OFF genes are randomly positioned. bQ computed from the empirical gene expression profile and randomized profiles. The horizontal axis shows the value of the objective function and the vertical axis is the probability density function. The 12 subplots correspond to 12 individual cell lines: A549, CAKI2, G401, NCI-H460, PANC-1, RPMI-7951, SJCRH30, SK-MEL-5, SK-N-DZ, T-47D, GM12878 and K562 respectively. In each subplot, the red square indicates the value for the empirical profile, the histogram shows the distribution for values obtained from an ensemble of randomized profiles. c For cell lines GM12878 and K562, an additional ensemble of randomized profiles was generated by shuffling gene indices within TADs alone. The resultant distribution is shown in brown. d Optimization of Q using a Monte Carlo procedure. Starting from the empirical gene expression profile, there is room for increasing Q for each of the cell lines tested

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