ArticlePloS one2009
Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs.Scientific reports · 2020Article
- Classification and Computational Analysis ofFrontiers in genetics · 2020Article
- Fast Regulation of Hormone Metabolism Contributes to Salt Tolerance in Rice (Plants (Basel, Switzerland) · 2018Article
- Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs.PLoS neglected tropical diseases · 2017Article
- Impacts of the overexpression of a tomato translationally controlled tumor protein (TCTP) in tobacco revealed by phenotypic and transcriptomic analysis.Plant cell reports · 2017Article
- Grouping miRNAs of similar functions via weighted information content of gene ontology.BMC bioinformatics · 2016Article
- Eliciting the Functional Taxonomy from protein annotations and taxa.Scientific reports · 2016Article
- Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks.Methods (San Diego, Calif.) · 2016Article
- Proteomic Study of Entamoeba histolytica Trophozoites, Cysts, and Cyst-Like Structures.PloS one · 2016Article
- INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.Nucleic acids research · 2015Article
- A weighted multipath measurement based on gene ontology for estimating gene products similarity.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak.BMC infectious diseases · 2013Article
- The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.Evolutionary bioinformatics online · 2013Article
- Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes.BMC genomics · 2012Article
- Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.BMC bioinformatics · 2012Article
- Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana.Frontiers in plant science · 2012Article
- What evidence is there for the homology of protein-protein interactions?PLoS computational biology · 2012Article
- Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses.BMC plant biology · 2011Article
- A shortest-path graph kernel for estimating gene product semantic similarity.Journal of biomedical semantics · 2011Article
- The genome of the domesticated apple (Malus × domestica Borkh.).Nature genetics · 2010Article
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5 authors.
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Abstract
backgroundLarge-scale sequencing projects have now become routine lab practice and this has led to the development of a new generation of tools involving function prediction methods, bringing the latter back to the fore. The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. METHODOLOGY: We present here a novel method called ARGOT (Annotation Retrieval of Gene Ontology Terms) that is able to process quickly thousands of sequences for functional inference. The tool exploits for the first time an integrated approach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtained by different methods and in this work we have based ARGOT processing on BLAST results.
conclusionsThe extensive benchmark involved 10,000 protein sequences, the complete S. cerevisiae genome and a small subset of proteins for purposes of comparison with other available tools. The algorithm was proven to outperform existing methods and to be suitable for function prediction of single proteins due to its high degree of sensitivity, specificity and coverage.
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