RT Journal Article
SR Electronic
T1 <em>StateHub-StatePaintR</em>: rapid and reproducible chromatin state evaluation for custom genome annotation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 127720
DO 10.1101/127720
A1 Coetzee, Simon G.
A1 Ramjan, Zachary
A1 Dinh, Huy Q.
A1 Berman, Benjamin P.
A1 Hazelett, Dennis J.
YR 2017
UL http://biorxiv.org/content/early/2017/10/17/127720.abstract
AB Genome annotation is critical to understand the function of disease variants, especially for clinical applications. To meet this need there are segmentations available from public consortia reflecting varying unsupervised approaches to functional annotation based on epigenetics data, but there remains a need for transparent, reproducible, and easily interpreted genomic maps of the functional biology of chromatin. We introduce a new methodological framework for defining a combinatorial epigenomic model of chromatin state on a web database, StateHub. In addition, we created an annotation tool for bioconductor, StatePaintR, which accesses these models and uses them to rapidly (on the order of seconds) produce chromatin state segmentations in standard genome browser formats. Annotations are fully documented with change history and versioning, authorship information, and original source files. StatePaintR calculates ranks for each state from next-gen sequencing peak statistics, facilitating variant prioritization, enrichment testing, and other types of quantitative analysis. StateHub hosts annotation tracks for major public consortia as a resource, and allows users to submit their own alternative models.