ArticleBMC bioinformatics2008
Gene Ontology term overlap as a measure of gene functional similarity.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
74 citing papers in PubMed.
- Genomic and metabonomic insights into the lignin-degrading potential of a novel halophilic bacterial strain Salinicoccus sp. HZC-1.BMC genomics · 2025Article
- A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs.NPJ digital medicine · 2025Article
- Exact p-values for global network alignments via combinatorial analysis of shared GO terms : REFANGO: Rigorous Evaluation of Functional Alignments of Networks using Gene Ontology.Journal of mathematical biology · 2024Article
- Bayesian profile regression for clustering analysis involving a longitudinal response and explanatory variables.Methodology : European journal of research methods for the behavioral & social sciences · 2024Article
- Broad functional profiling of fission yeast proteins using phenomics and machine learning.eLife · 2023Article
- HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey.BMC bioinformatics · 2022Article
- Bayesian Multi-View Clustering given complex inter-view structure.F1000Research · 2022Article
- Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.Genome biology and evolution · 2021Article
- Comparative Analysis of Unsupervised Protein Similarity Prediction Based on Graph Embedding.Frontiers in genetics · 2021Article
- Multiple kernel learning for integrative consensus clustering of omic datasets.Bioinformatics (Oxford, England) · 2020Article
- UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization.PloS one · 2020Article
- A Literature Review of Gene Function Prediction by Modeling Gene Ontology.Frontiers in genetics · 2020Review
- Extended Multitarget Pharmacology of Anticancer Drugs.Journal of chemical information and modeling · 2019Article
- Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme.BMC bioinformatics · 2019Article
- Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm.International journal of molecular sciences · 2019Article
- A network biology approach to unraveling inherited axonopathies.Scientific reports · 2019Article
- Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network.Frontiers in genetics · 2019Article
- GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.Scientific reports · 2018Article
- Monitoring changes in the Gene Ontology and their impact on genomic data analysis.GigaScience · 2018Article
- A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks.EBioMedicine · 2018Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundThe availability of various high-throughput experimental and computational methods allows biologists to rapidly infer functional relationships between genes. It is often necessary to evaluate these predictions computationally, a task that requires a reference database for functional relatedness. One such reference is the Gene Ontology (GO). A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO).
resultsWe computed the TO for randomly selected gene pairs from the mouse genome. For comparison, we implemented six previously reported semantic similarity measures that share the feature of using computation of probabilities of terms to infer information content, in addition to three vector based approaches and a normalized version of the TO measure. We find that the overlap measure is highly correlated with the others but differs in detail. TO is at least as good a predictor of sequence similarity as the other measures. We further show that term overlap may avoid some problems that affect the probability-based measures. Term overlap is also much faster to compute than the information content-based measures.
conclusionOur experiments suggest that term overlap can serve as a simple and fast alternative to other approaches which use explicit information content estimation or require complex pre-calculations, while also avoiding problems that some other measures may encounter.
Indexed as
Identifiers
What OpenQuestion holds
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.