We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed infernal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data
Keywords for this software
References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- Oates, Chris.J.; Mukherjee, Sach: Network inference and biological dynamics (2012)
- Andrecut, M.; Kauffman, S.A.; Madni, A.M.: Evidence of scale-free topology in gene regulatory network of human tissues (2008)
- Xu, Rui; Venayagamoorthy, Ganesh K.; Wunsch II, Donald C.: Modeling of gene regulatory networks with hybrid differential evolution and particle swarm optimization (2007)
- Smith, V.Anne; Jarvis, Erich D.; Hartemink, Alexander J.: Influence of network topology and data collection on network inference (2002)