GrapHi-C: graph-based visualization of Hi-C datasets
نویسندگان
چکیده
منابع مشابه
GrapHi-C: Graph-based visualization of Hi-C Datasets
Background: Hi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or “interacting”). Typically, results from Hi-C experiments (whole-genome contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not intuitively represent the complex organization and folding of the genome in 3D space, making the ...
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UNLABELLED Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CH...
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Long-range chromosomal associations between genomic regions, and their repositioning in the 3D space of the nucleus, are now considered to be key contributors to the regulation of gene expressions, and important links have been highlighted with other genomic features involved in DNA rearrangements. Recent Chromosome Conformation Capture (3C) measurements performed with high throughput sequencin...
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Hi-C enables simultaneous detection of interaction frequencies between all possible pairs of restriction fragments in the genome. The Hi-C method is based on chromosome conformation capture (3C), which uses formaldehyde cross-linking to fix chromatin regions that interact in three-dimensional space, irrespective of their genomic locations. In the Hi-C protocol described here, cross-linked chrom...
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Graphs or networks provide a powerful abstraction to view and analyze relationships among different entities present in a dataset. However, much of the data of interest to analysts and data scientists resides in non-graph forms such as relational databases, JSON, XML, CSV and text. The effort and skill required in identifying and extracting the relevant graph representation from data is often t...
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ژورنال
عنوان ژورنال: BMC Research Notes
سال: 2018
ISSN: 1756-0500
DOI: 10.1186/s13104-018-3507-2