transitivity network analysis definition

Each gene is knocked out at least once and the expressions of the other genes are measured for each knockout experiment.

More concretely, in the context of genetic regulatory networks with knockout experiments, the nodes of the networks are genes. genes) are systematically perturbed and the effects on the other nodes are observed. They are usually based on perturbation experiments, e.g., gene knockouts or knockdowns, in which one or more network nodes (e.g. Techniques for the reconstruction of biological networks, such as genetic, metabolic or signaling networks, are used for getting insight into the inner mechanisms of the cell. Our experiments show that: i) taking into account the edge weights improves the reconstruction quality compared to the unweighted case ii) it is advantageous not to distinguish between positive and negative interactions since this lowers the complexity of the algorithms from NP-complete to polynomial without loss of quality. Parallel implementations of these algorithms can achieve speed-ups of two orders of magnitude compared to their sequential counterparts. This is a refinement of the removal condition for the unweighted graphs and avoids to a great extent the erroneous elimination of direct edges. A direct interaction is removed only if there exists an indirect interaction path between the same nodes which is strictly more certain than the direct one. Edge weights are regarded as uncertainties of interactions. We develop efficient scalable parallel algorithms for transitive reduction on general purpose graphics processing units for both standard (unweighted) and weighted graphs. They also exhibit the anomaly that some existing direct interactions are also removed. The existing algorithms for transitive reduction are sequential and might suffer from too long run times for large networks. Transitive reduction removes such relations if they can be explained by an indirect path of influences. Techniques for reconstruction of biological networks which are based on perturbation experiments often predict direct interactions between nodes that do not exist.

Transitivity network analysis definition