New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

Abstract

The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.

Modeling Regulatory Network Topology Improves Genome-Wide Analyses of Complex Human Traits

“…Since RSS-NET is a model-based approach, we designed a large array of simulation scenarios for both correctlyand mis-specified β. To reduce computation of this large-scale design, we mainly used real genotypes 28 of 348,965 genome-wide common SNPs and a whole-genome regulatory network inferred for B cell (436 TFs, 3,018 TGs) 20,29 . We also performed simulations on real genotypes 30 of 1 million common SNPs 31 or different networks, and obtained similar results.…”

“…To further investigate its real- Enrichment analyses of 38 networks across 18 traits. We first inferred 20 whole-genome regulatory networks for 38 human cell types and tissues (Methods; Supplementary Table 1) from public data 29 of paired expression and chromatin accessibility (PECA). On average each network has 431 TFs, 3,298 TGs and 93,764 TF-TG weighted edges.…”

“…Here we inferred 38 regulatory networks from context-matched high-throughput sequencing data of gene expression (e.g., RNA-seq) and chromatin accessibility (e.g., DNAse-seq or ATAC-seq). We obtained these PECA data from portals of ENCODE 29 We first constructed an "omnibus" network from PECA data of 201 biosamples across 80 cell types and tissues, using a regression-based method 20 . In brief, by modeling the distribution of TG expression levels conditional on RE accessibility levels and TF expression levels, we estimated a regression coefficient for each TF-TG pair.…”

“…where G j is the set of all genes within 1 Mb window of SNP j (a standard cis-eQTL window size 9,10,58 ), c j g measures the relative impact of a SNP j on gene g, T g is the set of all genes directly regulated by TF g in a given network (T g is empty if gene g is not a TF), and v gt measures the relative impact of a TF g on its TG t. Since a genome-wide analysis typically involves many SNPs and genes, we fix {T g , v gt , c j g } to ensure the identifiability of (5). We use inferred edges and weights of a context-specific TF-TG network 20,29 to specify T g and v gt respectively. We use context-matched cis-eQTL 9,10,58 to specify c j g (Supplementary Notes and Tables 17-18).…”

LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements

“…Encyclopedia of DNA elements (ENCODE) project announces >1.2 million candidate functional regulatory elements in human and mouse. This project shows that focusing on variants in regulatory elements within the non-coding regions can help to discover the real pathogenic variations ( 8 ). The ENCODE project has put forward a lot of novel insights on the regulated ways at the genome level, and identified many new types of regulatory elements such as TFBSs, enhancers, DNase I hypersensitive sites (DHSs), topologically associated domains (TADs), footprints and open chromatin regions ( 9 ).…”