ArticleBMC bioinformatics2020
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Genome-Wide DNA Methylation and RNA Analysis Reveal Epigenetic and Transcriptomic Changes in Carbapenem-Resistant Klebsiella pneumoniae Strains.Current microbiology · 2025Article
- Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives.Journal of advanced research · 2025Review
- Methylation changes of liver DNA during the formation of gallstones.Epigenomics · 2024Article
- Inter-individual variations in circadian misalignment-induced NAFLD pathophysiology in mice.iScience · 2024Article
- Comprehensive time-course gene expression evaluation of high-risk beef cattle to establish immunological characteristics associated with undifferentiated bovine respiratory disease.Frontiers in immunology · 2024Article
- Analysis of DNA Methylation Differences during the JIII Formation ofCurrent issues in molecular biology · 2023Article
- Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.Bioinformatics (Oxford, England) · 2023Article
- Identification and validation of a DNA methylation-driven gene-based prognostic model for clear cell renal cell carcinoma.BMC genomics · 2023Article
- Meliaceae genomes provide insights into wood development and limonoids biosynthesis.Plant biotechnology journal · 2023Article
- Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population ofFrontiers in plant science · 2022Article
- Comparative Transcriptome Analysis of the Expression of Antioxidant and Immunity Genes in the Spleen of a Cyanidin 3-O-Glucoside-Treated Alzheimer's Mouse Model.Antioxidants (Basel, Switzerland) · 2021Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists.Biology · 2021Article
- Multi-omics profiling highlights lipid metabolism alterations in pigs fed low-dose antibiotics.BMC genetics · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFunction genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis. While tools have been developed to identify biological functions that are enriched in the genes sets, there remains a need for comprehensive tools that identify functional enrichment of genes for both model and non-model species from a different function classification perspective.
resultsWe developed AllEnricher, a tool that calculates gene set function enrichment, with user-defined updatable libraries backing up for both model and non-model species as well as providing comprehensive functional interpretation from multiple dimensions, including GO, KEGG, Reactome, DO and DisGeNET.
conclusionsAllEnricher incorporates up to date information from different public resources and provides a comprehensive resolution for biologists to make sense out of specific gene sets, making it an advanced open-source tool for gene set function analysis.
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