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Each node in the network represents a single protein sequence, and each edge represents the pairwise connection with the most significant BLAST E-value (better than the cutoff) connecting the two sequences.
ESJ database was prepared by pairwise connection of exon sequences from every locus annotated by UCSC knownGene model (mm9, July, 2007).
Soft thresholding resulted in a 5,000 × 5,000 dimensional weighted adjacency matrix containing pairwise connection strengths.
We transformed the normalized expression value of the Pearson correlation into measures of pairwise connection strengths [ 12].
In these networks, the pairwise connection strength (adjacency) between 2 network nodes can be factored into node specific contributions, named node 'conformity'conformity
In a weighted network, the resulting Pearson correlation matrix is transformed into a adjacency matrix (aij = |cor xi, xj)| β ), which represent the pairwise connection strengths.
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In addition to the pairwise connections, each residue is connected to its native state so that the translational mode or the zero eigenvalue is stabilized.
The first network (1255 nodes, 5122 edges) was built to include the pairwise connections of the genes that were connected in all four networks.
Pairwise connections that show decreased entropy with age are depicted in Figure 5.
Pairwise connections between biological entities, instead of canonical pathways, can be exported from Moksiskaan.
The resulting network was sparse with 48,827 gene connections out of a maximum of approx. 37.4 million pairwise connections.
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