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Results: FunFHMMer generates more functionally coherent groupings of protein sequences than other domain-based protein classifications.
This implies that our algorithm can identify more functionally coherent gene clusters relating to specific TFs.
Isomap identified more functionally coherent clusters than PCA and captured more information in the first two-components.
Overall, the one from the proposed approach clearly has better modularity as illustrated in Figure 4, which may imply more functionally coherent network modules in it.
Since the SVM model can easily avoid falsely connecting functionally dissimilar proteins, the resultant interactions are expected to be more functionally coherent and can further improve protein annotation.
The structurally inferred interaction network is highly modular and more functionally coherent compared with experimental interaction networks derived from multiple literature citations.
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Although brain atlases obtained from cytoarchitecture or anatomy have long been used for this task, connectivity-driven methods have arisen only recently, aiming to delineate more homogeneous and functionally coherent regions.
Our functional analysis and comparison with HTP networks show that our structurally inferred interactions are more functionally and pathway coherent than interactions obtained by HTP screens.
Recent evidence based in clinical epidemiology, computational genomics and various model systems [ 17- 21] suggests that disease phenotypes emerge from dysfunction of one or more components of a functionally coherent gene module.
First, the methods capture the key properties that differentiate coherent gene sets from random ones GO terms in a functionally coherent gene set are more likely to be enriched and their functions are more closely related semantically and biologically.
This is encouraging because functionally coherent modules are more likely to be biologically relevant.
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more functionally important
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more functionally diverse
more functionally uniform
more functionally complete
more functionally similar
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more functionally meaningful
more functionally limited
more functionally independent
more functionally replete
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