ArticleBMC bioinformatics2006
Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Maternal slow-release nitrogen diets during late gestation optimize the energy metabolism in calves' skeletal muscle.PloS one · 2026Article
- Benchmarking multiple gene ontology enrichment tools reveals high biological significance, ranking, and stringency heterogeneity among datasets.Frontiers in bioinformatics · 2026Article
- Study on Antibacterial Activity of Water Extract of Galla chinensis Against Carbapenemase-Producing Enterobacteriaceae.MicrobiologyOpen · 2025Article
- Cerebrospinal fluid proteomic profiling of cognitively unimpaired individuals with suspected non-Alzheimer's disease pathophysiology.Brain communications · 2025Article
- CSF proteomic profiles of neurodegeneration biomarkers in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Dissecting the Immune System through Gene Regulation.Advances in experimental medicine and biology · 2024Article
- Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses.G3 (Bethesda, Md.) · 2023Article
- Impact of Maternal Feed Restriction at Different Stages of Gestation on the Proteomic Profile of the Newborn Skeletal Muscle.Animals : an open access journal from MDPI · 2022Article
- The Pathway Coexpression Network: Revealing pathway relationships.PLoS computational biology · 2018Article
- Classification of gene signatures for their information value and functional redundancy.NPJ systems biology and applications · 2018Article
- Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes.GigaScience · 2017Article
- Constellation Map: Downstream visualization and interpretation of gene set enrichment results.F1000Research · 2015Article
- A Bayesian extension of the hypergeometric test for functional enrichment analysis.Biometrics · 2014Article
- Glucan Biosynthesis Protein G Is a Suitable Reference Gene in Escherichia coli K-12.ISRN microbiology · 2011Article
- Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.PloS one · 2010Article
- Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets.BMC bioinformatics · 2010Article
- GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach.Bioinformatics (Oxford, England) · 2010Article
- Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data.BMC bioinformatics · 2009Article
- A general modular framework for gene set enrichment analysis.BMC bioinformatics · 2009Article
- Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.Nucleic acids research · 2009Article
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2 authors.
Funding
Abstract
backgroundGene Ontology (GO) terms are often used to assess the results of microarray experiments. The most common way to do this is to perform Fisher's exact tests to find GO terms which are over-represented amongst the genes declared to be differentially expressed in the analysis of the microarray experiment. However, due to the high degree of dependence between GO terms, statistical testing is conservative, and interpretation is difficult.
resultsWe propose testing groups of GO terms rather than individual terms, to increase statistical power, reduce dependence between tests and improve the interpretation of results. We use the publicly available package POSOC to group the terms. Our method finds groups of GO terms significantly over-represented amongst differentially expressed genes which are not found by Fisher's tests on individual GO terms.
conclusionGrouping Gene Ontology terms improves the interpretation of gene set enrichment for microarray data.
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