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HINT specifications


Unique identifier OMICS_11372
Alternative name Hmm-based IdeNtification of Tf footprints
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • Regulatory Genomics Toolbox


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  • person_outline Eduardo Gusmao <>

Publication for Hmm-based IdeNtification of Tf footprints

HINT in publications

PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] 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, […]

PMCID: 5467166
PMID: 28585545
DOI: 10.1038/ncomms15652

[…] 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 […]

PMCID: 5351933
PMID: 27798116
DOI: 10.1093/hmg/ddw369

[…] 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 […]

PMCID: 4787753
PMID: 26476451
DOI: 10.1093/nar/gkv1056

[…] 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 ; (,)). […]

PMCID: 4356053
PMID: 25763115
DOI: 10.1186/s13148-015-0057-5

[…] 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 […]

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HINT institution(s)
IZKF Computational Biology Research Group, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Computational RNA Biology Lab and Bioinformatics Core, Max Planck Institute for Biology of Ageing, Cologne, Germany; Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany; Center of Informatics, Federal University of Pernambuco, Recife, Brazil
HINT funding source(s)
Interdisciplinary Center for Clinical Research (IZKF Aachen), RWTH Aachen University Medical School, Aachen, Germany; and Brazilian research agencies: FACEPE and CNPq

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