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1.
Figure 2

Figure 2. From: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.

Correlation coefficient matrices of intra-chromosomal interactions. Left, middle and right panel represent colored heat map of correlation coefficient matrices of chromosome 20 intra-chromosomal interactions (1 Mb resolution) in control condition, E2-treated condition, and between control and E2-treated conditions, respectively. Here positive and negative correlation coefficients are color scaled to red and green, respectively.

Junbai Wang, et al. BMC Genomics. 2013;14:70-70.
2.
Figure 4

Figure 4. From: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.

Dynamical changes of chromosomal interactions between control and E2-treated conditions. Number of gained (i.e. red smooth line, positive value) and lost (i.e. blue smooth line, negative value) interactions between control and E2-treatd conditions are calculated for every 1 Mb region of human genome based on the four types of the strongest chromosomal interactions (i.e. strong differential gain or loss chromosomal intra or inter interactions, Additional file 7).

Junbai Wang, et al. BMC Genomics. 2013;14:70-70.
3.
Figure 5

Figure 5. From: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.

Association of chromosomal interaction frequency and ER-alpha binding motifs. ER-alpha binding motifs are identified by applying peak calling program wBELT on public available ER-alpha Chip-Seq experiments. Then the number of ER-alpha binding motifs in every 1 Mb region of human genome is plotted against to the rank order of local chromosomal interaction frequencies in Hi-C experiments. Figures from the left to the right represent such plot in Hi-C control, E2-treated, E2-treated gained interaction only and E2-treated lost interaction only conditions, respectively.

Junbai Wang, et al. BMC Genomics. 2013;14:70-70.
4.
Figure 3

Figure 3. From: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.

Distribution of relative ratios of chromosome interaction changes. Upper panel: Histogram of relative ratios (chromosomal interaction changes in 1 Mb resolution, E2-treated vs control condition). Lower panel: sorted relative ratios, red smooth line is relative ratio equals 0.67 (e.g., a 2 fold change) and green smooth line is relative ratio equals 1.33 (e.g., a 5 fold change). Non-interaction elements are excluded from analysis such as Z-score equals 0 in both control and E2-treated interaction matrices. A 10-fold interaction change is expected when the relative ratio equals 1.63, gain and lost interactions are equivalent to the relative ratio 2 and −2, respectively.

Junbai Wang, et al. BMC Genomics. 2013;14:70-70.
5.
Figure 1

Figure 1. From: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.

Chromosomal interaction hotspots. Upper panel: intra-chromosomal interaction for chromosome 20 at control condition; down panel: intra-chromosomal interaction for chromosome 20 at E2-treated condition; right panel, red smooth line represents detected number of ERα binding sites in the region (1 Mb resolution), and blue smooth line is the maximum read counts in the region (1 Mb resolution); left panel, chromosomal interaction hot regions (within amplified regions) that identified by this study are colored by blue bar at X-axis and Y-axis, respectively; positive and negative Z-scores are colored by red and green color, which indicate the observed chromosome region has higher and lower interaction frequency than the average, respectively.

Junbai Wang, et al. BMC Genomics. 2013;14:70-70.
6.
Figure 6

Figure 6. From: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.

A heat map of change of histone modifications between E2-treated and control conditions for four types of chromosomal interactions. Here T-values are obtained by perform t-test for genes that were chosen by the identified four types of chromosomal interaction changes (e.g., gain strong inter-chromosomal interaction, loss strong inter-chromosomal interaction, gain strong intra-chromosomal interaction and loss strong intra-chromosomal interaction, detailed information please refer to Additional file 7). The T-test was used to evaluate significance of dynamical change of various marks between E2-treated and control conditions (1 Mb resolution), positive and negative T-values are colored by yellow and blue, respectively. In the figure, 0, +1 and −1 represent E2 treated condition vs. control condition at gene body, 5 kb upstream and 5 kb downstream, respectively.

Junbai Wang, et al. BMC Genomics. 2013;14:70-70.

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