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This is done so as to give disconnected nodes a value for calculations of connectivity but keeping it significantly larger than the observed maximum distance; so we chose the number 17. Disconnected target genes are not counted, and do not affect the average.
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The calculation of connectivity intensity is executed along with the cluster-forming operation.
The connectivity group is responsible for the calculation of all connectivity descriptors.
A preliminary calculation of network connectivity was used to identify the most connected probe for each gene.
This is of particular importance for the calculation of a connectivity index (see below) since the use of correlated measures essentially includes a related property twice in the index, thus potentially overemphasizing the importance of an individual within the network.
The above mentioned estimation of fiber direction distribution, subsequent probabilistic tractography and the calculation of regional connectivity were implemented using FSL4.1 software and our in-house scripts developed in the Matlab 7.8 platform.
The calculation of the connectivity was made using an in-house developed Perl script.
All following analyses took place on participants' individual modular decomposition and subsequent calculation of hub connectivity.
This type of meta-analysis a part of Interactome tool of the MetaCore and allows calculation of relative connectivity for a hub as a measure of interactions enrichment in experimental data vs. expected for a random data set of a similar size.
As stated above, the calculation of the probability of connectivity for a given road segment is based on the method proposed in CAR which can be formulated as P = 1 − ∑ k = max m − n, n 0 max m − n / n ′, n 0 C m k ⋅ C m − k × n ′ n C m n ⋅ ∑ l = 0 m C m l − 1 l ⋅ C m − k × n ′ n C m n 1 − ∑ i = k − n 0 min k, m − k ⋅ n 0 c i m − k C m k, (6).
Following calculation of the degree of connectivity, a gene co-expression network was generated and the genes clustered onto a topological overlap matrix (TOM), based on their dissimilarity.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com