The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The project has generated high-quality, genome-wide maps of several key histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues. This web portal serves as a supplementary data repository accompanying the flagship consortium paper titled Integrative Analysis of 111 reference human epigenomes (Nature, Feb. 2015). We provide uniformly processed datasets, integrative analysis products and interactive genome browser sessions resulting from a joint analysis of 111 consolidated epigenomes from the Roadmap Epigenomics Project and 16 epigenomes from The Encyclopedia of DNA Elements (ENCODE) project.
Release 9 of the compendium contains uniformly mapped datasets corresponding to each of the epigenomic data types spanning 183 biological samples. We refer to these as unconsolidated epigenomes since there often exist multiple samples (technical and biological replicates from multiple individuals and/or datasets from multiple centers) from a particular unique cell type or tissue. In order to reduce redundancy, improve data quality and achieve uniformity required for our integrative analyses, experiments were subjected to additional processing to obtain comprehensive data for 111 consolidated epigenomes (See Processed Data section for additional details). Numeric epigenome identifiers EIDs (e.g. E001) and mnemonics for epigenome names were assigned for each of the consolidated epigenomes. The metadata section summarizes the mapping of the unconsolidated Release 9 samples to the consolidated epigenome IDs and provides key metadata terms and quality control statistics. Datasets corresponding to 16 epigenomes from the ENCODE project (with epigenome IDs ranging from E114-E129) were also processed similarly and used in the integrative analyses, thus giving us a total of 127 consolidated epigenomes.
Select Initialize Grid Visualization to obtain a grid of uniformly processed data sets (columns) across all consolidated and/or unconsolidated epigenomes (rows).
Select data views (signal tracks, peak calls, read alignments)
Visualize in the epigenome browser
Epigenomes are ordered by groups (you can expand/hide groups by clicking +/-).
You can select different views of the data (signal tracks, peak calls, alignments)
Input track height for each data view in the text box.
EIDs correspond to consolidated epigenomes
If you unselect Ignore unconsolidated epigenome data, unconsolidated epigenomes will be appear in the rows in blue text.
NOTE: We do not recommend visualizing the consolidated datasets alongside the unconsolidated ones. Preferably visualize the consolidated datasets.
To select grid-cells (Selected grid-cells appear blue-grey)
- Click on a single grid-cell; or
- Click and drag across rows and columns of the grid to select a sub-matrix of the multiple grid-cells.
- Click on row or column header to select entire row or column
- You can perform each of these actions mutiple times to select multiple disjoint grid-cells, sub-matrices, rows or columns.
To unselect grid-cells(Unselected cells appear white)
- Click on selected cell to unselect it
- Click and drag across selected cells you want to unselect.
- Click selected row or column headers to unselect them.