ArticleBioinformatics (Oxford, England)2021
BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed.
- An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity.Database : the journal of biological databases and curation · 2024Trial
- Innate immune activation restricts priming and protective efficacy of the radiation-attenuated PfSPZ malaria vaccine.JCI insight · 2024Trial
- Article
- Immune Responses to Influenza Infection in Children.Open forum infectious diseases · 2026Article
- Assessing the translational relevance of specific molecular pathways in spontaneous lupus mouse models.Frontiers in immunology · 2026Article
- Ficoll-based isolation biases the profiling of immune cells and leukemic blasts in AML samples.Frontiers in immunology · 2026Article
- SLE-diseaseome: a comprehensive meta-collection of systemic lupus erythematosus relevant functional pathways.Bioinformatics advances · 2026Article
- Multi-omic analysis identifies biological processes underlying progressive interstitial lung disease in systemic sclerosis.The FEBS journal · 2025Article
- CMV-specific clonal expansion of Th1, GZMKbioRxiv : the preprint server for biology · 2025Article
- A Flexible and Responsive Remote Study Design to Assess Gene Expression Changes During Wildfire Smoke Exposure with homeRNA, an At-home Blood Sampling Kit.medRxiv : the preprint server for health sciences · 2025Article
- Targeting neutrophil-driven inflammation in adult-onset still's disease: molecular insights from gene expression profiles.Arthritis research & therapy · 2025Article
- Whole-Blood Longitudinal Molecular Profiling Maps the Road of Graft Versus Host Disease (GVHD).Cancers · 2025Article
- Blood molecular subtypes to guide precision treatment strategies in systemic juvenile idiopathic arthritis.Arthritis research & therapy · 2025Article
- Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood.Analytical chemistry · 2025Article
- Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood.bioRxiv : the preprint server for biology · 2024Article
- Entire expressed peripheral blood transcriptome in pediatric severe malarial anemia.Nature communications · 2024Article
- A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings.Database : the journal of biological databases and curation · 2024Article
- Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.Frontiers in immunology · 2024Article
- Human MCTS1-dependent translation of JAK2 is essential for IFN-γ immunity to mycobacteria.Cell · 2023Article
- High-temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines.Science advances · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
motivationWe previously described the construction and characterization of fixed reusable blood transcriptional module repertoires. More recently we released a third iteration ('BloodGen3' module repertoire) that comprises 382 functionally annotated modules and encompasses 14 168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires.
resultsWe have developed and describe here an R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. AVAILABILITY AND IMPLEMENTATION: The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.