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PubMed Central, Figure 1: Oncogene. 2016 Nov 3; 35(44): 5781–5794. Published online 2016 May 2. doi:  10.1038/onc.2016.112
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PMC full text:
Oncogene. Author manuscript; available in PMC 2016 Nov 7.
Published in final edited form as:
Oncogene. 2016 Nov 3; 35(44): 5781–5794.
Published online 2016 May 2. doi:  10.1038/onc.2016.112

Figure 1

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TNF-α promotes genome-wide cREL, p63α and TAp73 binding activities in the regulatory regions

(A) UM-SCC46 cells were treated with TNF-α (20 ng/ml) for 1 h to induce altered cREL, p63, and p73 protein expression in the nucleus. Oct-1 was used as the loading control. (B) ChIP-seq was performed using antibodies against cREL, p63α, and TAp73 for the UM-SCC46 cells treated (TNF) and untreated (NT) with TNF-α. The pulled-down DNAs were sequenced by the high-throughput sequencer GAIIx from Illumina. Total peak numbers (left) and peak-bound genes (right) are presented in the bar graph. (C) Characterization of the modulation of TF binding in the regulatory regions. The distribution of binding peaks in different regions of the genome is presented in the pie charts, and peak numbers are labeled at the top. The upper panel shows the percentages of the peaks distributed among regulatory (promoter, TTS, intragenic) and intergenic regions. The lower panel shows the percentages of the peaks distributed only among the different intragenic regions. (D) The binding peak numbers of each TF were plotted within 20 kb upstream (−) and downstream of the TSSs across the whole genome. The blue line is the basal transcription factor binding without TNF-α treatment; while the green line is after TNF-α treatment. (E) The transcription factor binding sites within 1 kb distance were identified, and the number of overlapping sites are presented in the Venn diagrams. (F) Distance relationships between two peak sets under different conditions in the ChIP-seq experiments were analyzed. Intersected peaks were defined to be within 1kb distance on the same chromosome. Y axis shows the quantity of intersected peaks at different intersection distance in bp (x axis). Blue, untreated; green, TNF-α treated.

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