b, Genome browser snapshot of enhancer activity and TF binding at the BBC3 gene locus in GP5d and HepG2 cells, demonstrating the excellent signal-to-noise ratio of the STARR-seq data. Both plus and minus-strand STARR-seq signal is shown, as well as ATAC-seq coverage and ChIP-seq for...
n, Chromatin-accessibility profiles across cell lines and HNF4A, FOXA2 and CEBPB ChIP-seq coverage on the SPP1 locus, with region-to-gene links and the SPP1 enhancer highlighted. For box-plots in b, e–g and i, the top/lower hinge represents the upper/lower quartile and whiskers ...
there are annotations of features such as repeats, SNPs, CpG islands etc. The light weight genome viewer (lwgv) is used to display the annotations of features at a given genomic locus. This tool also allows navigation to other resources on the web, such as NCBI [4...
Numbers after taxa names indicate numbers of corresponding representative species/genomes. The percentage shows the relative number of genomes with a single-copy TR (in red) or 2, 3, 4 and 5 and more TR copies (in shades of blue). Selection of plant species indicating presence of an ...
Requirement:genepopedit functions through the manipulation of multi-locus diploid SNP files structured in theGenepopfile formatlink. Specifically, we use thethree numberformat (e.g. 110110) where the six digits correspond to the alleles of a given locus for an individual. Locus names can be list...
distance of the elements in the network of chromatin contacts (with gP and gE being in the gene locus, PiE interacting directly, and EiE interacting indirectly with it). The robustness of these networks of direct co-dependencies, their ability to explain gene expression, and their correspondence...
Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes). Gene The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides ...
Likewise, this gene locus was represented on the microarray by multiple probes, which were both up and down regulated in the IMF4 cows. Three genes (ATOX1, COL1A1, and COL1A2) identified as down regulated in the IMF4 library were also identified as down regulated by microarray analysis. ...
Hepatocyte pseudobulk accessibility profiles (from periportal to pericentral) at the Axin2 locus are shown as an example; with predicted TF-binding sites, region-to-gene links coloured by SCENIC+ correlation score and gene expression across the zonated hepatocyte classes (from periportal to ...
(e.g., p53; see also Peng et al.42) or a set of closely bound TFs that fit between or associate directly with well-ordered nucleosomes43. The prevalence of both the closed-chromatin enhancers and chromatin-dependent enhancers suggests that they may contribute substantially to regional control...