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Our network integration experiments started with the combination of the six binary gene networks described in Section 2.2 (that is all the available gene networks excluding real-valued semantic similarity-based nets), using the unweighted combination methods presented in Section 2.4.2.
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All correlations were performed using Spearman's rank correlation and we combined probabilities using the unweighted Z-method [24].
Clustering analysis was performed using the unweighted pair group method with arithmetic mean clustering algorithm (UPGMA) to calculate the dendrograms of each DGGE gel and a combination of all gels.
In both scenarios, using the unweighted features, the worst results were reached.
The interobserver agreement of anatomical variations was analysed using the unweighted Cohen's kappa coefficient.
The band patterns were compared using the Dice-coefficient by using the unweighted pair group method to determine band similarity.
Cluster analysis was performed using the unweighted pair group method with the averages algorithm (UPGMA) [ 18].
Individual samples were then clustered within each of the five trees using the unweighted UniFrac method.
Dendrograms were generated using the unweighted pair-group method with arithmetic averages (UPGMA) calculation.
A dendrogram was generated by using the unweighted pair group method with arithmetic averages (UPGMA).
Dendrograms were created by using the unweighted pair group method with arithmetic averages.
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