ArticleNucleic acids research2011
NOA: a novel Network Ontology Analysis method.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- NetCrafter: ontology-derived gene network modeling and functional interpretation.Briefings in bioinformatics · 2026Article
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- LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data.Bioinformatics (Oxford, England) · 2023Article
- PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression.PLoS computational biology · 2023Article
- TLSEA: a tool for lncRNA set enrichment analysis based on multi-source heterogeneous information fusion.Frontiers in genetics · 2023Article
- PhenoExam: gene set analyses through integration of different phenotype databases.BMC bioinformatics · 2022Article
- Detecting the Critical States of Type 2 Diabetes Mellitus Based on Degree Matrix Network Entropy by Cross-Tissue Analysis.Entropy (Basel, Switzerland) · 2022Article
- COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.Briefings in bioinformatics · 2022Article
- Identifying biomarkers for breast cancer by gene regulatory network rewiring.BMC bioinformatics · 2022Article
- Inferring causal gene regulatory networkFrontiers in bioengineering and biotechnology · 2022Article
- Network-based prioritization of cancer biomarkers by phenotype-driven module detection and ranking.Computational and structural biotechnology journal · 2022Article
- Dependence of Graphene Oxide (GO) Toxicity on Oxidation Level, Elemental Composition, and Size.International journal of molecular sciences · 2021Article
- Comparative and mechanistic toxicity assessment of structure-dependent toxicity of carbon-based nanomaterials.Journal of hazardous materials · 2021Article
- ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in Endothelial Cells.Frontiers in physiology · 2021Article
- Toxicity of Single-Walled Carbon Nanotubes (SWCNTs): Effect of Lengths, Functional Groups and Electronic Structures Revealed by a Quantitative Toxicogenomics Assay.Environmental science. Nano · 2020Article
- Integrated Analysis Revealed Prognostic Factors for Prostate Cancer Patients.Medical science monitor : international medical journal of experimental and clinical research · 2019Article
- Graphical Model Selection for Gaussian Conditional Random Fields in the Presence of Latent Variables.Journal of the American Statistical Association · 2019Article
- iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data.BMC bioinformatics · 2018Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene ontology analysis has become a popular and important tool in bioinformatics study, and current ontology analyses are mainly conducted in individual gene or a gene list. However, recent molecular network analysis reveals that the same list of genes with different interactions may perform different functions. Therefore, it is necessary to consider molecular interactions to correctly and specifically annotate biological networks. Here, we propose a novel Network Ontology Analysis (NOA) method to perform gene ontology enrichment analysis on biological networks. Specifically, NOA first defines link ontology that assigns functions to interactions based on the known annotations of joint genes via optimizing two novel indexes 'Coverage' and 'Diversity'. Then, NOA generates two alternative reference sets to statistically rank the enriched functional terms for a given biological network. We compare NOA with traditional enrichment analysis methods in several biological networks, and find that: (i) NOA can capture the change of functions not only in dynamic transcription regulatory networks but also in rewiring protein interaction networks while the traditional methods cannot and (ii) NOA can find more relevant and specific functions than traditional methods in different types of static networks. Furthermore, a freely accessible web server for NOA has been developed at http://www.aporc.org/noa/.
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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.