Genes with high connectivity (query genes) provide alternative routes to connect target nodes (i.e., mutations on these target nodes could be buffered by different queries).
To foster interest, it is also important to connect target content to everyday life (Keller, 1987).
To connect target genes with their regulators, one might then consult genome-wide chromatin immunoprecipitation data (ChIP-seq and ChIP-chip) to identify transcription factor binding events in promoters that may be involved in recruiting RNAP II (3, 38, 39) and cross-reference the bound sequences with those identified by DNaseI protection (40).
The input data comprised a table of connection results with node columns, connected target columns, and their connections.
Saturated neurons, with the allocated number of strongly connected targets, do not form further connections.
In order to improve this non-uniformity, we tilted the surface normal of the target 15 degree from a line connecting target and substrate.
Moreover, for connections with enrichment |score|>1.25 (i.e. P<0.002), more than half (28 out of 51, vs. 21.3% by random chance) of connected targets participate in at least one common pathway.
Such maturation-triggered pruning is crucial for preventing all neurons from being recruited into the second group; without it, all connections from the training neurons, however weak initially, are eventually strengthened to maturation due to the consistent activations of the training neurons and their strongly connected targets.
In many model systems the paradigm has been to perturb or mutate a single gene and observe what happens; pull-down or yeast two-hybrid experiments have the same aim, connecting target proteins to those which they bind to, while many in vitro studies have shown that perturbation of a single gene is usually associated with concerted changes in many genes.
The cytokine layer was constructed by connecting target genes to corresponding measured cytokines.
