Reconstructing Pathways in Large Genetic Networks from Genetic Perturbations
AbstractI present an algorithm that determines the longest path between every gene pair in an arbitrarily large genetic network from large scale gene perturbation data. As a by-product, the algorithm reconstructs all direct regulatory gene interactions in the network. The algorithm is recursive, and is built around a graph representation of genetic networks. Its computational complexity is O(nk2), where n is the number of genes in the network, and k is the average number of genes affected by a genetic perturbation. In practice, it can reconstruct all path lengths for a network of more than 6000 genes in less than 30 CPU seconds. It is able to distinguish a large fraction of direct regulatory interactions from indirect interactions, even if the quality of its input data is substantially compromised.
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Bibliographic InfoPaper provided by Santa Fe Institute in its series Working Papers with number 01-09-050.
Date of creation: Sep 2001
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Genomics; reverse engineering; microarrays;
This paper has been announced in the following NEP Reports:
- NEP-ALL-2001-10-16 (All new papers)
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