The CORE database utilizes ElemeNT algorithm to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements. For each analyzed transcript, the existence of a putative core promoter at the expected position relative to the TSS is indicated. If a putative element exists, its relative position and the score are denoted (position, score). If more than one putative element exists, all the possible elements are indicated, with a semicolon separator. For DPE, MTE and Bridge elements the denoted position is of the associated Inr, as these elements are functional only at the precise position relative to the Inr.
(including CAGE, RNAseq, RefSeq, FlyBase and EPDnew TSSs)
The list of GO biological proccesses with fold enrichment ≥4 can be downloaded here.
File content description:
CAGE_Hoskins sheet -
Annotation of core promoter elements among CAGE-defined Drosophila melanogaster TSSs, based on Hoskins et al. Peak shapes are reported in the original study.
RNAseq_Nechaev sheet -
Annotation of core promoter elements among RNAseq-defined Drosophila melanogaster TSSs, based on Nechaev et al.
The general frequencies of detected elements among both datasets. Both absolute numbers and frequencies are reported.
For CAGE data, the summary of the frequencies is presented separately for all tags, peaked, broad and unclassified datasets.
Both CAGE and RNA-seq are based on the dm3 reference genome.
Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome research 2011; 21:182-92.
Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 2010; 327:335-8.