1. Overview of the ChIP‐Atlas data set and computational processing
Overview of the ChIP‐Atlas data set and computational processing Numbers of ChIP‐seq and DNase‐seq experiments recorded in ChIP‐Atlas (as of May 2018), indicating the proportion of the data for each species derived from ENCODE, Roadmap Epigenomics, and other projects.Cumulative number of SRX‐based experiments recorded in ChIP‐Atlas. Data published before and after the launch of ChIP‐Atlas in December 2015 are shown in gray and black, respectively.Numbers of experiments according to antigen (top) or cell type (bottom) classes for human, fruit fly, and nematode data. PSC, pluripotent stem cell; CDV, cardiovascular.Overview of data processing. Raw sequence data are downloaded from NCBI SRA, aligned to a reference genome, and subjected to peak calling, all of which can be monitored with the genome browser IGV. All peak‐call data are then integrated for browsing via the “Peak Browser” function, and they can be analyzed for TR–gene (“Target Genes”) or TR–TR (“Colocalization”) interactions as well as subjected to enrichment analysis (“Enrichment Analysis”). All of the results are tagged with curated sample metadata such as antigen and cell type names. In the diagrams, gray components (circles, TRs; arrows, genes) indicate queries by the user, with colored components representing the returned results.
Shinya Oki et al. EMBO Rep. 2018;embr
© as stated in the article, figure or figure legend