Background: Biological knowledge, and therefore Gene Ontology annotation sets, for human genes is incomplete. Recent studies have reported that biases in available GO annotations result in biased estimates of functional similarities of genes, but it is still unclear what the effect of incompleteness itself may be, even in the absence of bias. Pairwise gene similarities are used in a number of contexts, including gene "functional similarity" clustering and the related problem of functional ontology structure inference, but it is not known how different similarity measures or clustering methods perform on this task, and how the clusters are affected by annotation completeness.
Liu et al. REF suggest that biases in the available GO annotations result in also biased estimates of gene functional similarities.
GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness
BMC Bioinformatics
BMC Bioinformatics
Computer Science Biology Medicine