Annotation source for visualization of result
hsun3163 opened this issue · comments
To generate the annotation in the above visualization, three types of annotation were used, all came from the built-in annotation of annotatr package
CpG Annotations:
Current: Given by the AnnotationHub package for the given organism.
Potential Improvement: Use the same annotation from sesame
FANTOM5 Permissive Enhancers:
Current: Permissive enhancers were determined from bi-directional CAGE transcription as in Andersson et al. (2014), and are downloaded and processed for hg19 and mm9 from the FANTOM5 resource.
Problem: Lacking many enhancers observed on UCSB Encode cCRE track, namely EH38E1877438 which near ACE promoter
Potential Improvement: Find the UCSB Encode cCRE from annotation hub
Genic Annotations
Current: Data from the txdb.hsapiens.ucsc.hg38.knowngene packages. Genic annotations include 1-5Kb upstream of the TSS, the promoter (< 1Kb upstream of the TSS), 5’UTR, first exons, exons, introns, CDS, 3’UTR, and intergenic regions
Made from resources at UCSC on 2022-09-27 15:30:34 +0000 (Tue, 27 Sep 2022) and based on the hg38 genome based on the knownGene table by Bioconductor Core Team