Semantic Similarity over the Gene Ontology F. M. Couto, M. J. Silva, P. M. Coutinho Family Correlation and Selecting Disjunctive Ancestors LASIGE - XLDB CIKM 2005 

Family Correlation Family similarity is also a structural similarity –Like sequence similarity, but: Overcomes some of the limitations of sequence similarity Since it is based on experimental results about protein domains Validate GO semantic similarity with family similarity Pfam similarity –a database of protein families –assigned to UniProt proteins

GraSM (Graph-based Similarity Measure) Motivation: –Semantic similarity measures use Gene Ontology as a hierarchical tree Approach: –Selecting multiple ancestors of two GO terms –Describe different interpretations Results:

Disjunctive Ancestors (t1,t2)  DisjAnc(t5) (t0,t1)  DisjAnc(t5) Since (t1,t2)  DisjAnc(t5) then CommonDisjAnc(t4,t5) = {t2,t1}

Biological Process Cellular ComponentMolecular Function

Biological Process Cellular ComponentMolecular Function

Conclusions Family correlation provided a measures’ ranking that is: – uniform over all the different aspects of GO –consistent with previous studies using different corpora We have demonstrated the higher effectiveness of GraSM for calculating semantic similarities between GO terms –Higher correlation using disjunctive common ancestors than only using the most informative common ancestor All the measures mentioned in this document were implemented by FuSSiMeG (Functional Semantic Similarity Measure between Gene-Products) –FuSSiMeG is available on the Web at: