Motivation: Ontologies are used in the annotation and analysis of biological data. As knowledge accumulates, ontologies and annotation undergo constant modifications to reflect this new knowledge. These modifications may influence the results of statistical applications such as functional enrichment analyses that describe experimental data in terms of ontological groupings. Here, we investigate to what degree modifications of the Gene Ontology (GO) impact these statistical analyses for both experimental and simulated data. The analysis is based on new measures for the stability of result sets and considers different ontology and annotation changes.
Results: Our results show that past changes in the GO are non-uniformly distributed over different branches of the ontology. Considering the semantic relatedness of significant categories in analysis results allows a more realistic stability assessment for functional enrichment studies. We observe that the results of term-enrichment analyses tend to be surprisingly stable despite changes in ontology and annotation.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/bts498 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools.
Bioinformatics
January 2025
Department of Biology, Emory University, Atlanta, GA 30322, United States.
Motivation: In silico functional annotation of proteins is crucial to narrowing the sequencing-accelerated gap in our understanding of protein activities. Numerous function annotation methods exist, and their ranks have been growing, particularly so with the recent deep learning-based developments. However, it is unclear if these tools are truly predictive.
View Article and Find Full Text PDFBuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis.
Database (Oxford)
January 2025
Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
Amidst the global challenge of extreme poverty, the livestock sector can significantly contribute to global sustainable development goals by enhancing resilience, smallholder productivity, and market participation. The Indian livestock sector is one of the largest in the world with a total livestock population of 535.82 million, ∼10.
View Article and Find Full Text PDFDeciphering the Transcriptional Metabolic Profile of Adipose-Derived Stem Cells During Osteogenic Differentiation and Epigenetic Drug Treatment.
Cells
January 2025
Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
Adipose-derived mesenchymal stem cells (ASCs) are commonly employed in clinical treatment for various diseases due to their ability to differentiate into multi-lineage and anti-inflammatory/immunomodulatory properties. Preclinical studies support their use for bone regeneration, healing, and the improvement of functional outcomes. However, a deeper understanding of the molecular mechanisms underlying ASC biology is crucial to identifying key regulatory pathways that influence differentiation and enhance regenerative potential.
View Article and Find Full Text PDFMEGA-GO: Functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network.
Bioinformatics
January 2025
Guangdong Provincial Key Laboratory IRADS, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, China.
Motivation: The increasing accessibility of large-scale protein sequences through advanced sequencing technologies has necessitated the development of efficient and accurate methods for predicting protein function. Computational prediction models have emerged as a promising solution to expedite the annotation process. However, despite making significant progress in protein research, graph neural networks face challenges in capturing long-range structural correlations and identifying critical residues in protein graphs.
View Article and Find Full Text PDFA meta-analysis of genome-wide association studies to identify candidate genes associated with feed efficiency traits in pigs.
J Anim Sci
January 2025
Department of Animal Science, Federal University of Viçosa, Viçosa, MG, 36570-900, Brazil.
Pig production is an agricultural sector of great economic and social relevance to Brazil and global markets. Feed efficiency traits directly influence the sustainability of pig production due to the economic impact of feed costs on the production system and the environmental footprint of the industry. Therefore, breeding for improved feed efficiency has been a target of worldwide pig breeding programs.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!