ArticleNucleic acids research2023
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed.
- Transcriptomic profiles of the maternal-to-zygotic transition for Drosophila embryos exposed to acute and chronic heat stress.G3 (Bethesda, Md.) · 2026Article
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- Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci.eLife · 2026Article
- RNA sequencing in adult Drosophila females identifies estrogen-related receptor-dependent transcriptional changes in metabolism, DNA replication, and translation.G3 (Bethesda, Md.) · 2026Article
- Beadex modulates haematopoiesis and innate immune defence against microbial infection in Drosophila melanogaster.Journal of cell science · 2026Article
- Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms.Molecular systems biology · 2026Article
- Disruption of small RNAs and mechanistic variation in Segregation Distorter: A sperm-killing drive system in Drosophila melanogaster.PLoS genetics · 2026Article
- Convergent genomic trajectories shape adaptation to life on land across animal lineages.Nature communications · 2026Article
- LipiDecipher: A Structure-Oriented Analytical Framework for Interpretable Clinical Lipidomics.Metabolites · 2026Article
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- Female genetic variation controlling timing of mating plug ejection inbioRxiv : the preprint server for biology · 2026Article
- Male reproductive biology was reshaped during placental mammal diversification through epididymal secretome expansion.EMBO reports · 2026Article
- Metabolism fine tuning and cardiokines secretion represent adaptative responses of the heart to High Fat and High Sugar Diets in flies.PLoS genetics · 2026Article
- RNA Sequencing in AdultbioRxiv : the preprint server for biology · 2026Article
- Genome-wide CRISPR knockout cell screening platform for the disease vector tick speciesbioRxiv : the preprint server for biology · 2026Article
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- GOLDEN fusion: a graph-oriented learning with domain-embedding network fusion for generating super gene sets in functional genomics.Briefings in bioinformatics · 2026Article
- The Cell Ontology in the age of single-cell omics.Scientific data · 2026Article
- Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking.Nature communications · 2026Article
11 more citing papers are in PubMed but not listed here.
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Abstract
Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.
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