ArticleBMC bioinformatics2012
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 348 papers.
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Who cites it
348 citing papers in PubMed.
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- Microfluidics-enabled proteomic profiling reveal iron-driven immune evasion by an antimicrobial-resistant pathogen.Cell reports methods · 2026Article
- Oleuropein-based olive leaf extract enhances muscle mitochondrial bioenergetics response to moderate - but not maximal - intensity exercise in humans.The Journal of physiology · 2026Article
- Proteome profiles of esophageal squamous cell carcinoma tie mitochondrial complex I to immunotherapy.EMBO molecular medicine · 2026Article
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- Chromatin association promotes UBR5-mediated degradation of Rb.bioRxiv : the preprint server for biology · 2026Article
- Deep visual proteomics uncovers nociceptor diversity and pain targets.Nature communications · 2026Article
- Metronidazole and ether derivatives target Helicobacter pylori via simultaneous stress induction and inhibition.Nature microbiology · 2026Article
- Comparison of technologies for manufacturing extracellular vesicles for therapeutic applications.Trends in biotechnology · 2026Article
- Hyaluronic Acid Decoration Facilitates CD44-Mediated Targeting and Alters Protein Corona Formation of Extracellular Vesicles.Journal of extracellular vesicles · 2026Article
- Phosphoregulation of the novel hemi-arrestin MAPK scaffold Sms1 prevents untimely mating.Nature communications · 2026Article
- UltraPlex-TMT: Expanding Isobaric Hyperplexing via Orthogonal Protease Cleavage.Journal of proteome research · 2026Article
- Proteomic analysis across Healthy-NAT-Tumor tissues uncovers clinically relevant biological events in esophageal squamous cell carcinoma.Briefings in bioinformatics · 2026Article
- Defining the reference proteomes for small extracellular vesicles and non-vesicular components.Nature cell biology · 2026Article
288 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
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Abstract
Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ontology terms, sub-cellular localization, presence of protein domains or membership in protein complexes. 2D annotation enrichment detects annotation terms whose members show consistent behavior in one or both of the data dimensions. This consistent behavior can be a correlation between the two data types, such as simultaneous up- or down-regulation in both data dimensions, or a lack thereof, such as regulation in one dimension but no change in the other. For the statistical formulation of the test we introduce a two-dimensional generalization of the nonparametric two-sample test. The false discovery rate is stringently controlled by correcting for multiple hypothesis testing. We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software.
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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.