Note that 40Kb is the resolution of the Hi-C data for the 7 cell lines and 14 primary tissues generated by Schmitt et al 2016. Internally, HUGIn identifies the 40Kb bin containing the Anchor Position user specifies. For both plots, the bin containing the Anchor Position is highlighted in gray. After typing in the Anchor Position, users can click the “RUN” button (in red) to generate the virtual 4C plot (by default), as well as a more compact heatmap plot (available when clicking on the Information Type box). Accepted Anchor Position includes SNP names in rs nomenclature (dbSNP version 147), chr:bp (e.g., the default chr5:53,298,025), and multiple gene IDs including the common name, RefSeq gene name, ensemble ID, and UCSC gene name. By default, this Anchor Position is set to chr5:53,298,025, which is the position of SNP rs6450176, associated with type 2 diabetes status and adiponectin level. In the GWAS context, this Anchor Position is mostly defined by a SNP ID. The first section is the “Anchor Position”, which defines the anchor of long range chromatin interactions. The main interface of HUGIn consists of the following four major sections (Figure 1 below).
HUGIn hosts a compendium of Hi-C data (Schmitt et al., 2016) mapped to the human reference genome hg19. User Tutorial User Interface Output Extracting Figures FAQs Back to Main Pageįor questions or comments about HUGIn, please contact jsmartin at. HUGIn is designed to explore chromatin organizations across multiple human cell lines and primary tissues.
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