Table 1.
A reference guide to the NIH Roadmap Epigenomic data resource.
| Download data? | Browse data with… | View data on… | Updated | Other features | Can upload own data? | Ref. | |
|---|---|---|---|---|---|---|---|
| Reference Epigenome Mapping Consortium Homepage | Links to data download | Clickable data matrix or visual data browser | Links to UCSC browser mirror (Epigenome Browser) | Data: at each data freeze (four-times per year) Other items: as needed | Protocols, publications, quality metrics, project and center/group information | No (but linked Epigenome Browser supports upload) | [103] |
| NCBI Epigenomics Hub | .wig | Sample (i.e., cell/tissue type) browser, experiment (i.e., epigenetic feature) browser, text search | NCBI epigenomics viewer or UCSC browser mirror | Continuously | `Compare Samples' tool to identify regions of greatest chromatin differences, suggests GO terms and pathways most associated | Being implemented | [106] |
| NCBI Gene Expression Omnibus | .bed, .wig, .bam and SRA | By sample, study or data matrix | NCBI Epigenomics viewer | Continuously | N/A | [105] | |
| The Human Epigenome Atlas (on Genboree) | .bed, .wig by ftp or http | By sample, assay or clickable data matrix | UCSC browser, Atlas Gene/Pathway browser (read densities across single genes or pathways) | At each data freeze | Information on metadata, data flow and data quality. Tools for analysis via Genboree workbench (independent tools and Galaxy pipelines). Data and functionality exposed via HTTP REST APIs for programmatic use and extension | [107] | |
| Roadmap Epigenomics Visualization Hub | No | ENCODE style data matrix | UCSC browser mirror, or remote display at UCSC main site (see [108], click `load track hub') | At each data freeze | UCSC mirror hosts integrative analysis tracks and summary tracks, tracks viewable at UCSC main site | Being implemented | [108,109] |
| Human Epigenome Browser at Washington University | Yes | Expandable data selection matrix and metadata matrix | Next-generation epigenome browser | At each data freeze | Google map-style zoom and pan, genomic data and metadata viewer, data collation view, pathway/gene set view, statistical analysis | Yes | [111] |
| Epigenome Browser UCSC mirror | .bed, .wig through table browser Individual reads not available | UCSC data selection matrix (ENCODE style) | UCSC browser mirror | At each data freeze | High-utility UCSC mirror tracks | Yes | [104] |
API: Application programming interface; ENCODE: Encyclopedia of DNA Elements; GO: Gene-ontology; HTTP: Hypertext transfer protocol; N/A: Not applicable; NCBI: National Center for Biotechnology Information; REST: Representational state transfer; SRA: Short Read Archive; UCSC: University of California-Santa Cruz.