In our browser, we use the queried region as bait (either a gene name or a SNP ID), and extract a row of Hi-C data centered on the bait region, hence, virtual 4C.ĬhIA-PET: another implementation of chromatin ligation-based method, which detects long-range interactions between genomic regions that are enriched for a feature (either histone modification or transcription factor binding). 4C data is plotted as a curve line, where the center is the bait region and a peak signal in distal region indicates there is a chromatin interaction event. Virtual 4C: Circular chromosomal conformation capture(4C) is a chromatin ligation-based method that surveys for one-vs-many interactions in the genome, that is, to measure the interaction frequencies between a bait locus of interest and any other loci. To facilitate users with this goal, we implemented the following three methods in our 3D Genome browser: For example, many users are interested in using Hi-C data to explore enhancer-promoter interactions. Identify Linkage between Genes, Enhancers and SNPs Although displaying Hi-C data as a heatmap is informative to visualize large genome structures such as TADs, it is not intuitive to show interactions between two specific loci. Simply click the "Check gene expression on the top right corner of this page. You can also conveniently check the expression for the queried the genes across over 100 cell types profiled by the ENCODE project. We observe that this known enhancer and the promoter of SHH are located within the same TAD and the long range interaction between them is also evident in the Hi-C map, marked by the black arrow In this region, there is a known enhancer (marked by green bar) that regulate the SHH gene17. In this case, we display the tracks for RNA-Seq and H3K27ac (active enhancer mark) ChIP-Seq data for the same cell type. Under the heatmap, we also imbed the UCSC genome browser for the same region, so that the users can explore both the chromatin interaction and other "omics" data simultaneously. To make the Hi-C interaction more visible, users can conveniently adjust the color bar on the same page. Once the initial HiC heatmap is displayed, there are several other function buttons to further assist users to explore around this region, such as zoom in/out and move to right/left.
In Figure below, we display the 25kb resolution Hi-C matrix, published in Rao et al Cell 2014. For Hi-C data with multiple resolutions (bin sizes), there is another dropdown menu for users to choose the appropriate size according to their needs. Our browser auto-fills gene names as users type, based a variety of gene annotations, including refSeq, UCSC and ensemble gene sets.Īfter clicking the submit button, the Hi-C interactions in GM12878 for the queried gene are shown on the right panel. We can visualize this region by selecting human and hg19 from the drop-down for species and genome assembly, and then typing in the gene name SHH in the textbox.
#Ucsc genome browser how to
Here we demonstrate how to query the chromatin interactions for regions surrounding SHH (Sonic Hedgehog) gene.
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