ArticleBioinformatics (Oxford, England)2025
TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Authors and funding
4 authors.
Funding
Abstract
motivationNon-coding RNA (ncRNA) plays a crucial role in gene regulation, including by forming sequence-specific RNA-DNA interactions at gene regulatory elements. One form of interaction takes place via the formation of RNA:DNA:DNA triple helices (triplexes). Accurate computational prediction of triplex formation from nucleotide sequences is an important tool in ncRNA research but remains somewhat inaccessible and complex. To address this, we created TripLexicon, a web-based interface for accessing and analyzing predicted gene regulatory RNA-DNA interactions in human and mouse.
resultsPredicted interactions can be accessed from RNA-, DNA-, and region-centric perspectives. For each RNA transcript, visualizations at genome and nucleotide resolution are available, providing insight into target genes and regions, as well as putative functional domains of the transcript. Predicted target genes can immediately be subjected to ontology and pathway enrichment analysis, providing rapid insight into potential functions mediated by the RNA-DNA interactions of the queried transcript. DNA and region queries are designed to identify potentially important ncRNA interactors at sites of interest. AVAILABILITY AND IMPLEMENTATION: TripLexicon is accessible at https://triplexicon.uni-frankfurt.de. This website is free and open to all users and there is no login requirement. All data and code is uploaded to Zenodo: https://zenodo.org/records/17143608 and the code for the webserver is available on Github: https://github.com/SchulzLab/TripLexicon.
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What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.