AI Article Synopsis
- A new algorithm was developed to measure functional similarity among gene products using gene ontology (GO) annotations, which have a hierarchical structure.
- The algorithm outperformed existing methods in terms of performance evaluation, and it has been implemented in a software package called FSim that runs on the R environment.
- FSim provides a user-friendly way to identify functionally related genes for individual genes or sets of genes based on GO data.
Article Abstract
Background: During the analysis of genomics data, it is often required to quantify the functional similarity of genes and their products based on the annotation information from gene ontology (GO) with hierarchical structure. A flexible and user-friendly way to estimate the functional similarity of genes utilizing GO annotation is therefore highly desired.
Results: We proposed a novel algorithm using a level coefficient-weighted model to measure the functional similarity of gene products based on multiple ontologies of hierarchical GO annotations. The performance of our algorithm was evaluated and found to be superior to the other tested methods. We implemented the proposed algorithm in a software package, FSim, based on R statistical and computing environment. It can be used to discover functionally related genes for a given gene, group of genes, or set of function terms.
Conclusions: FSim is a flexible tool to analyze functional gene groups based on the GO annotation databases.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145548 | PMC |
| http://dx.doi.org/10.1155/2014/509149 | DOI Listing |
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