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. 2006 Oct 20;2(10):e139. doi: 10.1371/journal.pcbi.0020139

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© 2006 McManus et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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EDF and density plots are shown for pairwise comparison of NN distances (see text and Table 2 for details). The density plot represents density estimates of the NN distance distribution (NCBP to CBP) for nuclear components taken pairwise. KS is the p-value in the Kolmogorov-Smirnov test, while MW refers to the Mann-Whitney statistic.

(A) EDF plot comparing acetylated Lys5 (K5) and Lys12 (K12) of histone H4. No statistical difference is observed, suggesting that CBP is as close to both K5 and K12 foci.

(B) Density distribution plot for the same pairwise comparisons showing a similar trend as in (A).

(C) EDF plot comparing NN distances for CBP to FU and ARNA3. The FU foci distribution is significantly different from the ARNA3 foci, suggesting that CBP is closer to PolII than to nascent mRNA transcripts. Note the shape of the FU distribution at smaller CBP NN distances, indicating that a subpopulation of FU foci lie close to CBP foci.

(D) Density distribution plot for the same comparison. Note the bimodal distribution for FU, indicating a population of FU foci that lie closer to CBP than active PolII and could represent sites of active transcription.