ReviewNature protocols2024
Using clusterProfiler to characterize multiomics data.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 979 papers.
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
979 citing papers in PubMed.
- Whole Blood Transcriptomic Response to Perioperative Dexamethasone in Total Knee Arthroplasty: A Targeted Panel Analysis.Acta anaesthesiologica Scandinavica · 2026Trial
- NAD+ augmentation by nicotinamide riboside engages SLIT2/ROBO1 signaling to attenuate Th17 inflammation in psoriasis.JCI insight · 2026Trial
- Key molecular networks underlying retinol's biphasic effects on cell proliferation through multi-omics integrative analysis using genome-scale metabolic modeling.Synthetic and systems biotechnology · 2027Article
- CXCL13-expressing CD4Oncoimmunology · 2026Article
- Article
- A systematic transcriptomic atlas and predictive framework for metabolite-driven T cell state transitions.iScience · 2026Article
- A scalable, high-throughput glue perturbation screening platform for molecular glue discovery.iScience · 2026Article
- Single-cell transcriptomic atlas of the human fetal uveal tract reveals heterogeneity in melanocyte populations.iScience · 2026Article
- Splicing genes as main targets of differential splicing.G3 (Bethesda, Md.) · 2026Article
- Metrnl Reduces Thrombosis and Acute Myocardial Injury Through Inhibition of Platelet Activation via CD36 Receptor Degradation.Circulation · 2026Article
- Single-cell and spatial transcriptomics identify a JUNB+ neutrophil subset enriched in immune-excluded regions of lung adenocarcinoma.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Single-Nucleus Atlas of Spinal Sarcopenia Patients Reveals Disruption of Quiescent and Regenerative Satellite Cell Niches in Fatty-Infiltrated Muscle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The landscape of allele-specific expression in human kidneys.Science advances · 2026Article
- Adipose triglyceride lipase driven lipolysis as a targetable metabolic vulnerability in prostate cancer with intrinsic metabolic inflexibility.British journal of cancer · 2026Article
- Active transcriptome remodeling underlies antimony-induced drug tolerance in persister-like Leishmania parasites.PLoS pathogens · 2026Article
- Article
- Maternal epigenetic regulation of embryonic patterning in plants.Nature plants · 2026Article
- Comprehensive Analysis of miRNAs and Predicted Protein Interaction Networks in Skeletal Muscle Development of Myostatin-Deficient Rabbits.Animal genetics · 2026Article
- Multimodal Ageing Biomarkers and Plasma Proteomic Signatures Associated With All-Cause Mortality.Aging cell · 2026Article
- The transcriptional cortical response to daily torpor inLife science alliance · 2026Article
919 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors.
Funding
Abstract
With the advent of multiomics, software capable of multidimensional enrichment analysis has become increasingly crucial for uncovering gene set variations in biological processes and disease pathways. This is essential for elucidating disease mechanisms and identifying potential therapeutic targets. clusterProfiler stands out for its comprehensive utilization of databases and advanced visualization features. Importantly, clusterProfiler supports various biological knowledge, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, through performing over-representation and gene set enrichment analyses. A key feature is that clusterProfiler allows users to choose from various graphical outputs to visualize results, enhancing interpretability. This protocol describes innovative ways in which clusterProfiler has been used for integrating metabolomics and metagenomics analyses, identifying and characterizing transcription factors under stress conditions, and annotating cells in single-cell studies. In all cases, the computational steps can be completed within ~2 min. clusterProfiler is released through the Bioconductor project and can be accessed via https://bioconductor.org/packages/clusterProfiler/ .
Indexed as
Identifiers
39019974What 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.