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In total, 25 genes were not peripheral (i.e. they mediated at least one gene connection).
GR augments our a priori knowledge about gene connection using microarray experiment data.
Therefore, we next utilized IPA to establish a functional gene connection network with all the up-regulated genes enriched in the IPA 'Proliferation of cells' category (Supplementary material online, Table S3 ).
In current study, if a gene connection is presented more than the threshold value θ in repeated modeling, the connection is added into a final gene regulatory network with the value of parameters equal to the average of those in the repeated modeling.
To identify a star module, FunMod calculates the sub-network centralization (CE) using the formula: (3) CE = n (n - 2 ) × max (k ) n - 1 - GD where max(k) is the highest degree of central gene connection in the sub-network and n is the number of genes in the sub-network.
In addition, we demonstrated the lower expression of BCL10 in leprosy lesions than normal skins and a significant gene connection between BCL10 and the eight previously identified leprosy loci that are associated with NFκB, a major regulator of downstream inflammatory responses, which provides further biological evidence for the association.
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Within network clusters, inter-molecular relationships were deconstructed and quantified based on local module connectivity (n, n = number of direct gene connections) to weigh hubs according to neighborhood prioritization.
Hub inter-relationships were quantified based on local module connectivity, and calculated as the total number of direct gene connections representing a weighted importance of each signaling relay in cardiac differentiation pathways (see Materials and Methods).
First, we use yeast cell-cycle microarray data to compare results obtained when complexes-to-single gene connections are not taken into account and when they are.
In the absence of such information, we performed an initial validation of the network by searching for known gene connections in databases.
Individual gene connections can be difficult to visualize in such complex graphs as presented.
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