ArticleBiology2021
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists.
Article in Biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- Dry side of the core: a meta-analysis addressing the original nature of the ABA signalosome at the onset of seed imbibition.Frontiers in plant science · 2023Pooled it
- GOATEA: gene set enrichment analysis in R with shiny interactive visualizations.BMC bioinformatics · 2026Article
- Chicken microRNA 26a-5p regulates replication of Newcastle disease virus by direct targeting of the viral polymerase.Virology journal · 2026Article
- ASTRA: a comprehensive resource of stress-induced transcriptional activity in human cell lines.Nucleic acids research · 2026Article
- Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations.Computational and structural biotechnology journal · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Kidney whole-transcriptome profiling in primary antiphospholipid syndrome reveals complement, interferons and NETs-related gene expression.Rheumatology (Oxford, England) · 2024Article
- VC-resist glioblastoma cell state: vessel co-option as a key driver of chemoradiation resistance.Nature communications · 2024Article
- A genomics perspective of personalized prevention and management of obesity.Human genomics · 2024Review
- MFGE-8 identified in fetal mesenchymal-stromal-cell-derived exosomes ameliorates acute hepatic failure pathology.iScience · 2023Article
- Article
- Review
- Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.Bioinformatics (Oxford, England) · 2023Article
- Arena3DNAR genomics and bioinformatics · 2023Article
- PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach.BMC bioinformatics · 2023Article
- Article
- PRO-Simat: Protein network simulation and design tool.Computational and structural biotechnology journal · 2023Article
- SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data.Computational and structural biotechnology journal · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Phospholamban R14del disease: The past, the present and the future.Frontiers in cardiovascular medicine · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases, or phenotypes. Despite the variety of existing tools, most of them can process a single list per time, thus making a more combinatorial analysis more complicated and prone to errors. In this article, we present FLAME, a web tool for combining multiple lists prior to enrichment analysis. Users can upload several lists and use interactive UpSet plots, as an alternative to Venn diagrams, to handle unions or intersections among the given input files. Functional and literature enrichment, along with gene conversions, are offered by g:Profiler and aGOtool applications for 197 organisms. FLAME can analyze genes/proteins for related articles, Gene Ontologies, pathways, annotations, regulatory motifs, domains, diseases, and phenotypes, and can also generate protein-protein interactions derived from STRING. We have validated FLAME by interrogating gene expression data associated with the sensitivity of the distal part of the large intestine to experimental colitis-propelled colon cancer. FLAME comes with an interactive user-friendly interface for easy list manipulation and exploration, while results can be visualized as interactive and parameterizable heatmaps, barcharts, Manhattan plots, networks, and tables.
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.