2013
DOI: 10.1093/bioinformatics/btt120
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CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks

Abstract: The CytoHiC plugin, source code, user manual, example files and documentation are available at: http://apps.cytoscape.org/apps/cytohicplugin

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Cited by 17 publications
(12 citation statements)
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“…Interacting gene networks were built using CytoHiC with a resolution of 500 kb [25] . We first investigated interacting genes involved in ER α binding events to better understand the role of ER α -mediated E2 effect on functional chromatin interactions and conformation.…”
Section: Resultsmentioning
confidence: 99%
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“…Interacting gene networks were built using CytoHiC with a resolution of 500 kb [25] . We first investigated interacting genes involved in ER α binding events to better understand the role of ER α -mediated E2 effect on functional chromatin interactions and conformation.…”
Section: Resultsmentioning
confidence: 99%
“…To visualize networks of interacting loci, we used the CytoHiC plug-in of Cytoscape ( http://www.cl.cam.ac.uk/~ys388/CytoHiC/ ) [25] . Interacting loci were annotated using gene positions and ER binding sites to visualize networks of interacting genes and networks of ER bound interactions, respectively.…”
Section: Methodsmentioning
confidence: 99%
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“…This representation, despite being simple from a mathematical point of view, makes difficult to capture the complexity of the nuclear organization, since it only provides a description of binary interactions, preventing the creation of a metric about the distances of different genomic segments. To improve the analysis of HT-3C data, graph-based approaches have been proposed, such as CytoHi-C (Shavit, 2013) and Homer (Heinz et al, 2010), which both rely on Cytoscape for network analysis.…”
Section: Introductionmentioning
confidence: 99%
“…Therefore, it is necessary to partition the genome into large scale bins, and pool the reads falling into each pair of bins to generate a Hi-C contact matrix at a lower resolution level, in which each off-diagonal entry represents the number of paired-end reads spanning two different bins. In the exploratory data analysis, the Hi-C contact matrix, which is the input of all the downstream Hi-C analysis, can be visualized as a heat map using software HiTC [80], CytoHiC [81] and the WashU Epigenome Brower [82]. …”
Section: Overview Of Hi-c Experiments and Hi-c Data Preprocessing Procmentioning
confidence: 99%