GO-based Functional Dissimilarity of Gene SetsReport as inadecuate




GO-based Functional Dissimilarity of Gene Sets - Download this document for free, or read online. Document in PDF available to download.

BMC Bioinformatics

, 12:360

Sequence analysis applications

Abstract

BackgroundThe Gene Ontology GO provides a controlled vocabulary for describing the functions of genes and can be used to evaluate the functional coherence of gene sets. Many functional coherence measures consider each pair of gene functions in a set and produce an output based on all pairwise distances. A single gene can encode multiple proteins that may differ in function. For each functionality, other proteins that exhibit the same activity may also participate. Therefore, an identification of the most common function for all of the genes involved in a biological process is important in evaluating the functional similarity of groups of genes and a quantification of functional coherence can helps to clarify the role of a group of genes working together.

ResultsTo implement this approach to functional assessment, we present GFD GO-based Functional Dissimilarity, a novel dissimilarity measure for evaluating groups of genes based on the most relevant functions of the whole set. The measure assigns a numerical value to the gene set for each of the three GO sub-ontologies.

ConclusionsResults show that GFD performs robustly when applied to gene set of known functionality extracted from KEGG. It performs particularly well on randomly generated gene sets. An ROC analysis reveals that the performance of GFD in evaluating the functional dissimilarity of gene sets is very satisfactory. A comparative analysis against other functional measures, such as GS and those presented by Resnik and Wang, also demonstrates the robustness of GFD.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-12-360 contains supplementary material, which is available to authorized users.

Download fulltext PDF



Author: Norberto Díaz-Díaz - Jesús S Aguilar-Ruiz

Source: https://link.springer.com/







Related documents