… matrices of most transcription factors lack sufficient predictive … transcription factors and
demonstrate their utility in genome-… covered by at least 20 allelic reads in ChIP–seq experiments …

… and enhancer regions of genomic DNA and either activate or … tools to be installed or lack
effective visualisations, providing … CiiiDER will read sequences directly from data entered in …

… genome-wide [1], and DNase-seq, which identifies genome-… between the presence and
absence of epigenetic markers, … measure as the fraction of reads that fall into conservative peaks …

… TF binding sites in the genome, using tools like PWMscan [67], … transcriptional states and
response to signaling. However, the exact nature of these networks is unknown and we still lack …

… -DREAM in vivo Transcription Factor Binding Site Prediction … for a total of 31 transcription
factors in 22 primary cell types and … peaks are available due to the lack of replicates. In such …

… Transcription factors (TFs) are key cellular components that … of the genome where they can
recruit transcriptional co-factors … Therefore, the identification of TFBSs in genomic sequences …

… clean reads to human reference genome GRCh38. Datasets with <5 million reads after the
… (IgG samples were used as controls only at the absence of input samples). The peak calling …

… enriched in ChIP sample (~55%) vs the whole genome 44 (~41… p value < 0.001, **p value
< 0.01, the absence of asterisks … seq reads were aligned to the human reference genome with …

… million compact genomic elements that encode transcription factor … Currently we lack a
comprehensive, nucleotide-resolution … , with a mean of 4.3 footprints per DHS with sufficient read …

… Since plant genomes contain many classes of TFs absent from TFClass, we expanded the
TF structural classification using TFClass guidelines (39) and published structural evidence (…