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Semantic Similarity: Semantic Similarity was assessed using Gene Ontology term overlap (in Data S1) and by the Dice-Jaccard index (Gene Ontology overlap normalized by the number of terms attached to gene A plus the number of terms in gene B).
There is no gold standard method to assess network performance, but the Dice-Jaccard index attempts to correct for prevalence/multifunctionality (it is normalized to number of terms), and thus it tends to reduce IPN contribution over other methods, such as GO term overlap.
Raw counts of GO term overlap can be found in Additional file 27: Figure S16.
Our empirical algorithm first counted the GO term overlap for targets of an input miRNA list.
One such measure is the Term Overlap (TO), which considers the number of common terms between genes [ 47].
Parameters of cluster analysis were as follows: similarity term overlap 10, similarity threshold 0.50, initial and final group membership 3, multiple linkage threshold 0.5, and enrichment thresholds 0.01.
Similar(33)
The staff often mediated disputes, Mr. Kean said, recalling that when his term overlapped with Mr. Carey's, the New York governor was facing a budget crisis and sought his support on a proposal to sell the World Trade Center and divide the proceeds.
The term overlapping channels [1] (or non-orthogonal channels) is used to describe a relation between at least two channels that share a frequency range.
By contrast, the measures of concurrency that capture the impact of long term overlaps – point prevalence, overlap duration, and coital frequency – showed consistent differences across all of these populations that lined up with all of the observed HIV prevalence differentials.
Links that were confirmed three or more times between different experiments had significantly higher GO term overlaps than those seen only once or twice (p < 10-15) [ 15].
The term overlaps, but is not completely synonymous, with the family of illnesses referred to as juvenile chronic arthritis and/or juvenile idiopathic arthritis in Europe.
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