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The possibility of functional enrichment in the genes that make up the observed trans-eQTL clusters was assessed through testing of their GO annotations using the functional annotation clustering component of the web-based genetic data analysis tool DAVID (http://david.abcc.ncifcrf.gov) [28], [34].
The actual sequence clustering component of SEED is an iterative process consisting of three major steps.
The underlying components of NaviClusterCS are (i) an ultrafast graph clustering component, (ii) a property-based clustering component, and (iii) a visualization component that connects to the Cytoscape canvas.
Our method consists of three components: an ultrafast graph clustering component, a property-based clustering component, and an interface that presents an abstracted view and permits researchers to flexibly choose nodes/clusters (Fig. 1).
The new clusters resulting from the property-based clustering are used in the next component instead of those generated by the ultrafast graph clustering component, thereby reducing the number of clusters on the screen.
Finally, the clustering component manages all subcomponents described above.
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Table 12 Predicted values for automatically clustered component factor and Gr_component Error metric LR RPART NNR AC MC AC MC AC MC RSQ 0.98 0.76 0.80 0.7045 2.02 1.92 AIC 6586 6187 6461 6139 7033 6733 PRED 33.88 34.12 33.48 32.6915 0.48 0.67 AC is for automatic clustering of components and MC is for manual clustering of components.
Cancerous networks of oncogenes in humans are known to form a giant, highly clustered component in the whole signaling network [ 47].
We found in this study an insignificant small difference in the performance of the prediction models that automatically cluster components and the ones that use semantically clustered components instead.
Furthermore, we observed that the giant component of our disease map as well as the vicinities of obesity, T1DM, and T2DM clustered components of the cardiometabolic syndrome.
To analyze paralog expansion, we clustered components the same as the "simplified" cadhesome, except for ACTN1/4/SPTBN1 and the MAGUK proteins, which were more broadly clustered based on similar, but not exact type, number, and order of domains.
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