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Information
| Unique identifier | OMICS_11372 |
|---|---|
| Name | HINT |
| 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 |
Subtool
- Regulatory Genomics Toolbox
Versioning
No version available
Maintainer
- person_outline Eduardo Gusmao
Publication for Hmm-based IdeNtification of Tf footprints
HINT citations
(6)Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes
[…] 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 […]
Sox5 regulates beta cell phenotype and is reduced in type 2 diabetes
[…] 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 […]
Most brain disease associated and eQTL haplotypes are not located within transcription factor DNase seq footprints in brain
[…] 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 […]
Epigenetic program and transcription factor circuitry of dendritic cell development
[…] 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). […]
MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome wide signatures
[…] 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 […]
Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites
[…] 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 […]
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