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Table 1 Best combinations of similarity and clustering methods for recovering the known structure of GO classes

From: GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness

Annotation completeness

Type of GO classes

Best combinations

Clustering methods

Semantic similarity measure

complete

cellular

HAC

JiangConrath MAX

DAG

Relevance MAX, JiangConrath BMA, Lin BMA

multicellular

HAC

Resnik MAX, Weighted Jaccard, Weighted Cosine

DAG

Lin BMA

incomplete

cellular

HAC

JiangConrath MAX, Weighted Cosine

DAG

Lin BMA, Lin MAX, Relevance MAX, Resnik MAX

multicellular

DAG

Lin BMA, Relevance MAX