G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery
نویسندگان
چکیده
We have developed a set of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, and for further discovering biomedical knowledge from the GO database. The tools have been used for about 6.9 million times by 417 institutions from 43 countries since October 2006. The online tools are available at: http://bioinformatics.clemson.edu/G-SESAME.
منابع مشابه
A new method to measure the semantic similarity of GO terms
MOTIVATION Although controlled biochemical or biological vocabularies, such as Gene Ontology (GO) (http://www.geneontology.org), address the need for consistent descriptions of genes in different data sources, there is still no effective method to determine the functional similarities of genes based on gene annotation information from heterogeneous data sources. RESULTS To address this critic...
متن کاملProteInOn: A Web Tool for Protein Semantic Similarity
Bioinformatics arose from the need to manage and extract knowledge from the vast amount of sequence data generated by automated Molecular Biology techniques. One important step for this was the development of the Gene Ontology (GO), which provided a unified and structured vocabulary to describe proteins, and also a background to compare them, contributing to the integration of knowledge from th...
متن کاملIncorporating Biological Domain Knowledge into Cluster Validity Assessment
This paper presents an approach for assessing cluster validity based on similarity knowledge extracted from the Gene Ontology (GO) and databases annotated to the GO. A knowledge-driven cluster validity assessment system for microarray data was implemented. Different methods were applied to measure similarity between yeast genes products based on the GO. This research proposes two methods for ca...
متن کاملGene Ontology Similarity Measures Based on Linear Order Statistics
The standard method for comparing gene products (proteins or RNA) is to compare their DNA or amino acid sequences. Additional information about some gene products may come from multiple sources, including the set of Gene Ontology (GO) annotations and the set of journal abstracts related to each gene product. Gene product similarity measures can be based on evaluating sets of descriptor terms fo...
متن کاملGS2: an efficiently computable measure of GO-based similarity of gene sets
MOTIVATION The growing availability of genome-scale datasets has attracted increasing attention to the development of computational methods for automated inference of functional similarities among genes and their products. One class of such methods measures the functional similarity of genes based on their distance in the Gene Ontology (GO). To measure the functional relatedness of a gene set, ...
متن کامل