ArticleBMC bioinformatics2016
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Sensogenomics of music and Alzheimer's disease: An interdisciplinary view from neuroscience, transcriptomics, and epigenomics.Frontiers in aging neuroscience · 2023Pooled it
- Assessing the therapeutic potential of PDE-5 inhibitors in adults: Insights from a multi-omics study.Physiological reports · 2026Article
- M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress.Cell death and differentiation · 2026Article
- pyVIPER: a fast and scalable Python package for protein activity estimation and master regulator analysis of single-cell RNA sequencing data.BMC bioinformatics · 2026Article
- Effect of carbohydrate substrates on growth and enterotoxin gene expression in Bacillus cereus (pacificus).Scientific reports · 2025Article
- Thyrotropin Directly Affects Cardiac Electrophysiology and Is Associated With AF Prevalence.Circulation. Arrhythmia and electrophysiology · 2025Article
- Neurotranscriptomic profiling of deformed wing virus-infected honey bee foragers (Apis mellifera) with different cognitive abilities.Biology open · 2025Article
- Article
- DistinctFrontiers in immunology · 2025Article
- Neuronal activity-dependent gene expression is stimulus-specific and changes with neuronal maturation.Frontiers in molecular neuroscience · 2025Article
- Article
- E.PathDash, pathway activation analysis of publicly available pathogen gene expression data.mSystems · 2024Article
- Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2024Article
- Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark.Nature communications · 2024Article
- Article
- Eomes expression identifies the early bone marrow precursor to classical NK cells.Nature immunology · 2024Article
- Artificial intelligence-based epigenomic, transcriptomic and histologic signatures of tobacco use in oral squamous cell carcinoma.NPJ precision oncology · 2024Article
- BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.Nature biotechnology · 2024Article
- DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery.Briefings in bioinformatics · 2024Article
- 5'-Isoforms of miR-1246 Have Distinct Targets and Stronger Functional Impact Compared with Canonical miR-1246 in Colorectal Cancer Cells In Vitro.International journal of molecular sciences · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEnrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes. However, the often subtle benefits and disadvantages of the individual methods are confusing for most biological end users and there is currently no convenient way to combine methods for an enhanced result interpretation.
resultsWe present the EnrichmentBrowser package as an easily applicable software that enables (1) the application of the most frequently used set-based and network-based enrichment methods, (2) their straightforward combination, and (3) a detailed and interactive visualization and exploration of the results. The package is available from the Bioconductor repository and implements additional support for standardized expression data preprocessing, differential expression analysis, and definition of suitable input gene sets and networks.
conclusionThe EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. It combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.