Description
ChIP-Atlas is an integrative and comprehensive database for visualizing and making use of public ChIP-seq data. It covers almost all public ChIP-seq data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA, and is based on over 76,000 experiments, which is originally provided at http://chip-atlas.org/.
This track is an alternative view of the ChIP-seq peaks provided in the original site.
update: 2018-07-17
Display Conventions and Configuration
The color of individual peaks are bsaed on their significance levels (-log10(Pvalue)), from red (very significant ~ 1000), green (moderate ~500) , to blue (weak ~0).
Each of the peak pages have additional informaton, P value (- log10 scaled) as its score and their accessions to the repositories (SRA, ERA, or DRA). By following the link from the accession, you can see its detail on the ChIP-Atlas site.
Methods
The details of the peak calling and annotations are described in the documentation of ChIP-Atlas.
The resulting bigBed files are organized into a directory, and configured for trackHub by using dirHub.
Credits
ChIP-Atlas is developed by Oki S. et al. Please follow its document for the contents. The trackHub configuration is made by Kawaji H.
References
- Shinya Oki, Tazro Ohta, et al. Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions. bioRxiv 262899; doi: https://doi.org/10.1101/262899
- Oki, S; Ohta, T (2015): ChIP-Atlas. http://dx.doi.org/10.18908/lsdba.nbdc01558-000
- Kawaji H. "dirHub: a trackHub configurator with directory structure projection", bioRxiv 314807, doi: https://doi.org/10.1101/314807