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. 2015 Feb 11;6:40. doi: 10.3389/fgene.2015.00040

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Copyright © 2015 Merelli, Tordini, Drocco, Aldinucci, Liò and Milanesi.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Gene clustering analysis. Neighborhood graphs of the human leukocyte antigen (HLA) cluster of genes (cytoband chr6.p31.21) in four different runs from the Hi–C experiments of Dixon et al. (2012) to show inter and intra run modifications of the chromatin conformation. Panels (A,B) concern sequencing runs from hESC (SRA:SRR400260, SRA:SRR400261), while data in (C,D) are from IMR90 (SRA: SRR400266, SRA:SRR400267). In these graphs, seed genes are the genes given as input to the algorithm, while output genes are differentially represented according to their importance (in terms of degree).