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To facilitate the identification of nodes with the highest scores we applied the 'plot by centrality' feature of CentiScaPe.
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Thus, the main use of the 'plot by centrality' feature is to identify group of nodes clustered according to combination of specific topological and/or experimental properties, in order to extract sub-networks to be further analyzed.
Centroid is a complex centrality feature based on the ranking of how many nodes are closer to the gene than other genes in the network.
As there are 8 node centrality features and 1 edge centrality feature, each interaction is represented by a vector of 17 features, with the first 16 corresponding to the node centralities of the two proteins and the 17th corresponding to the edge centrality.
Centrality features were calculated to additionally estimate the load of the reactions.
We computed the centrality features by using the R package 'igraph' [ 59] consisting of betweenness centrality (BC), closeness centrality (CN), eccentricity (EC) [ 10], and eigenvector centrality (EV) [ 60].
Except for the centrality features and clustering coefficients, the topology features were calculated by a representation of the network as a bipartite graph consisting of metabolites and reactions as alternating nodes.
To better understand the basis of neurodegenerative diseases, we set out to study the centrality related features of proteins whose genes were differentially expressed (seed proteins) in MS and AD with respect to their protein neighbors.
Many theoretical models predict how node-level outcomes vary with the 'position' of a node in the network, captured by node varying network statistics such as centrality; or with features of the node's local neighbourhood such as node clustering; or with the 'connectivity' of the network, represented by statistics that vary at the network level such as network density.
A distinctive feature of Tsongkhapa's mature philosophy is the centrality he accords hermeneutics, and the particular stratification of philosophical systems it occasions.
We argue that a distinguishing feature of the Smart City concept is the centrality of people or the welfare of city residents.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com