ArticleScientific reports2018
Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.BMC bioinformatics · 2026Article
- CCL5 hiCD4+ T Cells Regulate Macrophage Polarization and Promote Immunotherapy Response in Bladder Cancer.Cancer research · 2026Article
- Synergistic Changes in Ascorbic Acid and Soluble Sugar Contents in Apricot Fruits and the Related Regulatory Mechanisms.Food science & nutrition · 2025Article
- Structural analysis of genomic and proteomic signatures reveal dynamic expression of intrinsically disordered regions in breast cancer.iScience · 2024Article
- OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.Nucleic acids research · 2024Article
- Bioinformatics and system biology approaches to determine the connection of SARS-CoV-2 infection and intrahepatic cholangiocarcinoma.PloS one · 2024Article
- Pan-Cancer Analysis Reveals Functional Similarity of Three lncRNAs across Multiple Tumors.International journal of molecular sciences · 2023Article
- Anti-inflammation is an important way that Qingre-Huazhuo-Jiangsuan recipe treats acute gouty arthritis.Frontiers in pharmacology · 2023Article
- An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations.Briefings in bioinformatics · 2022Article
- Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with different rooting depth responses to drought stress in potato.Frontiers in plant science · 2022Article
- Predicting candidate genes from phenotypes, functions and anatomical site of expression.Bioinformatics (Oxford, England) · 2021Article
- Inducing Apoptosis and Suppressing Inflammatory Reactions in Synovial Fibroblasts are Two Important Ways for Guizhi-Shaoyao-Zhimu Decoction Against Rheumatoid Arthritis.Journal of inflammation research · 2021Article
- Graph embeddings on gene ontology annotations for protein-protein interaction prediction.BMC bioinformatics · 2020Article
- Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics.Molecular genetics and genomics : MGG · 2020Article
- Article
- Methylation ofTranslational cancer research · 2020Article
- Evolving knowledge graph similarity for supervised learning in complex biomedical domains.BMC bioinformatics · 2020Article
- A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain.Database : the journal of biological databases and curation · 2020Article
- Regulatory Network Analysis to Reveal Important miRNAs and Genes in Non-Small Cell Lung Cancer.Cell journal · 2020Article
- Article
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3 authors.
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Abstract
There exists a plethora of measures to evaluate functional similarity (FS) between genes, which is a widely used in many bioinformatics applications including detecting molecular pathways, identifying co-expressed genes, predicting protein-protein interactions, and prioritization of disease genes. Measures of FS between genes are mostly derived from Information Contents (IC) of Gene Ontology (GO) terms annotating the genes. However, existing measures evaluating IC of terms based either on the representations of terms in the annotating corpus or on the knowledge embedded in the GO hierarchy do not consider the enrichment of GO terms by the querying pair of genes. The enrichment of a GO term by a pair of gene is dependent on whether the term is annotated by one gene (i.e., partial annotation) or by both genes (i.e. complete annotation) in the pair. In this paper, we propose a method that incorporate enrichment of GO terms by a gene pair in computing their FS and show that GO enrichment improves the performances of 46 existing FS measures in the prediction of sequence homologies, gene expression correlations, protein-protein interactions, and disease associated genes.
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