Hmm-based IdeNtification of Tf footprints

[…] 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, […]

[…] expected by chance. when comparing differential expression we used a chi-squared test to assess relationships between differentially expressed genes between studies., 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 […]

[…] ld thresholds. figure 6. , to consider whether biases in where dnase cuts across the genome influenced our results, we called footprints on brain dnase-seq datasets using a second algorithm, hint, that seeks to account for these biases (). although hint called substantially more footprints than wellington (median 880,341; range 845,115–1,035,430), intersecting these with sequence […]

[…] 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)., mpp were induced to differentiate in vitro into cdp (dc commitment) and further into cdc and pdc (dc subset specification; figure ; (,)). […]

[…] the projection test from the genometricorr package [] to find associations between dmr signatures and differentially expressed genes., 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 […]