ENCODE Software
All software used or developed by the ENCODE Consortium
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- WashU Epigenome Browser — sourceThe WashU Epigenome Browser provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap Epigenomics and the ENCODE projects. Browser features include: (i) visualization using virtual reality (VR), which has implications in biology education and the study of 3D chromatin structure; (ii) expanded public data hubs, including data from the 4DN, ENCODE, Roadmap Epigenomics, TaRGET, IHEC and TCGA consortia; (iii) a more responsive user interface; (iv) a history of interactions, which enables undo and redo; (v) a feature we call Live Browsing, which allows multiple users to collaborate remotely on the same session; (vi) the ability to visualize local tracks and data hubs. Amazon Web Services also hosts the browser at https://epigenomegateway.org/.Software type: database, other
- Regulatory Elements Database — sourceUsing an intuitive interface, you can 1) identify DNaseI-hypersensitive sites (DHS) within a genomic region of interest, 2) predict the target gene for DHS of interest, 3) predict the DHS that regulate a gene of interest, 4) identify clusters of similarly regulated DHS, that may have related function, 5) identify enriched motifs for transcription factors that may bind in these similarly regulated DHS, and 6) identify DHS that contain a DNA sequence motif for a transcription factor of interest. The Regulatory Elements Database provides access to roughly 2.8 million DNaseI-hypersensitive sites and their signal in 112 human samples, as well as Affymetrix microarray expression data for the same cell-types.Software type: database
- ENCODE-motifs — sourceA database that uncovers the molecular basis of TF binding in the human genome based on regulatory motif analysis of all Transcription Factors (TFs) grouped by family. This allows browsing of all known motifs for each factor, curated from TRANSFAC, Jaspar, and Protein Binding Microarray (PBM) experiments, and their enrichment and instances within corresponding TF binding experiments. It also provides a list of novel regulatory motifs discovered by systematic application of several motif discovery tools (including MEME, MDscan, Weeder, AlignACE) and evaluated based on their enrichment relative to control motifs within TF-bound regions. ENCODE-motifs also provides a genome-wide map of regulatory motif instances in the human genome for both known and novel motifs.Software type: database
- Factorbook — sourceFactorbook is a transcription factor (TF)-centric web-based repository of integrative analysis associated with ENCODE ChIP-seq data. It includes de novo discovered motifs, chromatin features surrounding ChIP-seq peaks (histone modification patterns, DNase I cleavage footprints, and nucleosome positioning profiles), deep-learned models of sequence features driving TF binding, and integration with GWAS variants and the ENCODE Registry of candidate cis-regulatory elements.Software type: database
- PIQ: Protein Interaction Quantification — sourcePIQ is a computational method that models the magnitude and shape of genome-wide DNase profiles to facilitate the identification of transcription factor (TF) binding sites. The input of PIQ is one or more DNase-seq experiments, the genome sequence of the organism assayed and a list of motifs represented as position weight matrices (PWMs) that describe candidate TF binding sites. PIQ uses machine learning methods to normalize input DNase-seq data and then predicts TF binding by detecting both the shape and magnitude of DNase profiles specific to each TF. The output of PIQ is the probability of occupancy for each candidate binding site in the genome, along with aggregate TF-specific scores (e.g. metrics for TF-specific chromatin opening).Software type: database
- RegulomeDB — sourceIdentifies DNA features and regulatory elements in non-coding regions of the human genome. One can enter dbSNP IDs, BED files, VCF files, or GFF3 files. A score is returned assessing the evidence for regulatory potential. Clicking on the score reveals the data supporting the inference, by data type and cell type. One can also click on hyperlinks to see the SNP or the region in the UCSC browser, ENSEMBL browser, and dbSNP.Software type: database, variant annotation
- HaploReg — sourceExplores annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Under Set Options tab, set Browse ENCODE button to "on" and select an LD threshold and reference population. Under Build Query Tab, enter a SNP (rsXXXXX), a set of SNPs, a genomic region, or select a GWAS from the drop down menu. HaploReg returns SNPs in LD with query SNPs, their frequency in 4 populations from 1000 Genomes Phase1, and also tells you what evidence ENCODE has found for regulatory protein binding (mouse over to see the protein names), chromatin structure (mouse over to see the cell types with DNase hypersensitivity), the chromatin state of the region (the chromatin state can predict an enhancer or promoter), and putative transcription factor binding motifs that are altered by the variant. Clicking on the SNP name hyperlink reveals further details, including cell type metadata and the mechanism of disruption/creation of TF binding regulatory motifs (showing the PWM matched and its alignment to the local sequence context). SNPs are also intersected with cross-species conserved elements, chromatin states from the Roadmap Epigenomics Consortium, and lead eQTLs from the GTEx Project browser.Software type: database, variant annotation