ArticleBMC genomics2025
Linkage: an interactive web application for linking of DNA regulatory peaks to genes.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed.
- ChromTag: an interactive R-shiny platform for analysis and visualization of CUT&Tag and ChIP-seq peak profiling data.Frontiers in bioinformatics · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
backgroundExisting studies have demonstrated that the integration analysis of transcriptomic and epigenomic data can be used to better understand the onset and progression of many diseases, as well as identify new diagnostic and prognostic biomarkers. However, such investigations on large-scale sequencing data remain challenging for researchers or clinicians with limited bioinformatics knowledge.
resultsTo facilitate the interpretation of the gene regulatory landscape, we developed an R Shiny application [Linking of atac-seq to gene expression data (Linkage)] for exploring and visualizing potential cis-regulatory elements (CREs) of genes based on ATAC-seq and RNA-seq data. Linkage offers six modules to identify, annotate, and interpret potential gene regulatory elements from the whole genome step by step. Linkage currently supports the analysis of human and mouse datasets. Linkage can provide interactive visualization for the correlation between chromatin accessibility and gene expression. More than that, Linkage identifies transcription factors (TFs) that potentially drive the chromatin changes through identifying TF binding motifs within the CREs and constructing trans-regulatory networks of the target gene set.
conclusionsThis powerful tool enables researchers to conduct extensive multi-omics integration analysis and generate visually appealing visualizations that effectively highlight the relationship between genes and corresponding regulatory elements. With Linkage, users can obtain publishable results and gain deeper insights into the gene regulatory landscape. AVAILABILITY AND IMPLEMENTATION: ‘Linkage’ is freely available as a Shiny web application https://xulabgdpu.org.cn/linkage . The source code and instructions for Linkage can be accessed via Github https://github.com/luoyyyy/Linkage .
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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 OpenQuestion graph.