Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation
Fig 5
Clusters and architectures identified by seqArchR for D. melanogaster, 6–8h AEL.
Sequence clusters arranged by the median interquantile widths (IQW) of CAGE TCs in seqArchR clusters (shortest on top, broadest at the bottom). From left to right: Box and whisker plots of per-cluster IQWs, TPMs, and PhastCons scores followed by per-cluster sequence logos, and stacked barplots showing proportion of TCs unique/shared between transitions. Sequence logos for histone gene clusters are shown with a grey background. ‘All’ denoting common between all stages. TPM, Tags per million.