Hmm-based IdeNtification of Tf footprints

[…] anscriptional cascades, to reduce false positive predictions of enhancer-promoter associations from open chromatin regions, the identification of DNase peaks will be modified using a new tool such as HINT [].In this study, I focused on three types of immune cells and stem cells such as H1-hESC and iPSC to examine transcriptional target genes in a genome scale, since in my previous study, I examine […]

[…] TFBS were detected using the Regulatory Genomics Toolbox (regen.googlecode.com). A region 1 kilobases (kb) upstream of the gene promoter (Ensembl built GRCh37.p13) was used to find binding sites. Next, a motif match analysis was […]

[…] ovide the best estimates of true binding sites and also, unlike some other DNase-seq footprinting methods, is not reliant on the presence of TF motifs (,). Other footprint-calling algorithms, such as HINT, additionally account for sequence-specific DNase cut biases and are likely to identify a larger proportion of footprints than Wellington (). These approaches rely on the imbalance in strand-spec […]

[…] e details in Supplementary Data). A further enrichment analysis was performed on footprints of cell-specific H3K4me1 peaks following Gusmao et al. (). This general workflow is based on tools from the Regulatory Genomics toolbox (www.regulatory-genomics.org). […]

[…] fferent cell types [].Some recent algorithms have already taken advantage of histone mark information to identify individual occurrences of known motifs, such as CENTIPEDE [], CHROMIA [], FIMO [] and HINT []. Considering a large collection of TFBSs and other CRMs (cis-regulatory modules) are still unrevealed, and sources like histone modification signals can be informative, there is some space to […]

[…] Transcription factor enrichment analysis was performed with the Regulatory Genomics Toolbox (http://www.regulatory-genomics.org). Regarding DMRs, we extended or shortened the regions to have a length of 40 bps. For up-/downregulated genes, we used 1-kb regions ups […]