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Phylogenetic profiling is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of genomes is used to infer a meaningful biological connection, such as involvement of two different proteins in the same biological pathway [35, 37].
3 11 In the current classification criteria for rheumatoid arthritis 3 "definite rheumatoid arthritis" is based on the confirmed presence of synovitis in at least one joint, absence of an alternate diagnosis better explaining the synovitis, and achievement of a total score of ≥6 (of a possible 10) on a scoring system.
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Gower's coefficient is preferential to the more commonly used Bray-Curtis coefficient (e.g. [30], [49], [50]) for this type of biochemical data because it treats zeros and non-zeros in the same way and joint absences between treatments are incorporated into the dissimilarity matrix [47].
As dissimilarity measure, Bray Curtis was used to account for the composition of the fungal communities as well as to exclude joint absences.
This finding can be explained by differences between the Jaccard and Yule's Q coefficients in how joint absences were treated (see Figure 1) [ 29].
Distance matrices were calculated using Jaccard distances for presence absence data, which is suitable for species analyses because it does not consider joint absences, whose meaning is confounded in ecological data (Legendre and Legendre 1998).
Given that 14 comorbidities were included in the cluster analysis, it would seem reasonable to treat joint absences as non-informative and exclude them from consideration as was the case with the Jaccard coefficient.
Several findings were supportive of the validity of the 28-joint count: (a) Absence of joint swelling on the 28-joint scale had a specificity of 98.1% and a positive predictive value (PPV) of 94.1% for the absence of swelling also on the 32-joint scale.
(4) Joint effusion (presence, absence).
(5) Joint swelling (presence, absence).
The preservation of the joint space and absence of juxta-articular osteoporosis are important clues in the differential diagnosis with rheumatoid arthritis [45].
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