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We determined high density modules in that network using the network clustering algorithm DPClusO [ 26] and found 1154 modules of size 3 or more (see Supplementary File 1 in supplementary material available online at http://dx.doi.org/10.1155/2014/154594).org/10.1155/2014/154594
We used pathways from KEGG database [ 14] and protein complexes from the MINT [ 15] database as 'known' functionally coherent modules, in that the proteins in these modules either perform related functions or form physical modules.
To properly assess methods which can produce overlapping modules, we chose performance measures that are based on protein pairs rather than modules; in that way, we avoid taking the same subset of nodes several times into account even if it occurs in more than one module.
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The hardware security module in that case must only handle table lookups; it can be implemented as its own module or also integrated into an existing hardware protected module or area (thus adding only little additional computational burden to the HSM already in use for other purposes).
Additionally, we predict the presence of aberrant HhH modules in RAD52 that are likely to be involved in DNA-binding.
But when the researchers created five modules that lumped together genes that were co-expressed, they found that the module in humans that's most closely tied to synapse formation and function had a "drastically" different developmental trajectory.
However, the quality of the modules obtained in that study suffered from the small number of samples and noisy input data.
This categorical description encompasses all reasonable definitions of modules; in particular, that of a group representation and that of a module over a Lie algebra.
Each matrix specifies, for each module in each child species (columns), the probability with which a gene conserved its module assignment in that species' immediate ancestor (rows), or was reassigned to another module.
To identify modules in dCTCF that mediate CP190 interaction, we first used the yeast two-hybrid assay.
Core TRR is similar to cis-regulatory module (CRM) in that both characterize functional regions by a cluster of regulatory elements.
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