G-SESAME

Gene Semantic Similarity Analysis and Measurement Tools

Tool Descriptions:

Since many biological data analysis methods require numeric representation of the functional similarity of genes, automatically discovering the descriptive similarities of genes and converting them into measurable numeric values are very important for such analyses.  This research project will solve this important problem by designing novel algorithms to measure the semantic similarity of vocabularies used to annotate genes and, in turn, devising effective algorithms to determine the functional similarity of genes. 

Based on these algorithms, the following online tools are implemented with more tools still under development:

1. Based on a novel method to encode a GO term's semantics into a numeric value by aggregating the semantic contributions of their ancestor terms (including this specific term) in the GO hierarchy, we implemented the following tools to measure the semantic similarity of GO terms:

   1. Semantic similarity of two GO terms.
   2. Semantic similarity of two GO term sets.

2. Based on the semantic correlation of GO terms used to annotate genes, we implemented the following tools to measure the functional similarity of genes:

   1. Functional similarity of two genes.
   2. Functional similarity for a set of genes.

3. Based on the gene functional similarity measurement, we implemented the following tools for gene functionality analyses:

   1. Cluster genes based on their functional similarities.

More tools are under development, we promise to bring them online as soon as possible.

Copyright © 2006-2007, G-SESAME Bioinformatics Group