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. 2010 Jan 8;6(1):e1000635. doi: 10.1371/journal.pcbi.1000635

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Peleg et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Edges represent functional relations with down-regulation relations depicted as regular arrows and up-regulations as cut-arrows. (A) LL-1: if knocking out genes or has a similar (opposite) effect on a shared target , then if affects the relation should be down-regulation (up-regulation). (B) LL-2: for two knocked out genes with at least two common targets , the respective influences should be either equivalent (bottom) or the exact opposite (top). (C) LL-3: If two genes affect each other then the effects should have equal signs. (D) The prevalence of the three properties in the original data and in randomized networks. (E) An example for the violation of LL-1 in the biosynthesis of steroids pathway. Two pathway members, ERG11 and ERG2, that increase each other upon knockout, have the exact same effect on all their common targets, down-regulating 110 genes (orange rectangle) and up-regulating 308 genes (green rectangle).

Inline graphic — Edges represent functional relations with down-regulation relations depicted as regular arrows and up-regulations as cut-arrows. (A) LL-1: if knocking out genes or has a similar (opposite) effect on a shared target , then if affects the relation should be down-regulation (up-regulation). (B) LL-2: for two knocked out genes with at least two common targets , the respective influences should be either equivalent (bottom) or the exact opposite (top). (C) LL-3: If two genes affect each other then the effects should have equal signs. (D) The prevalence of the three properties in the original data and in randomized networks. (E) An example for the violation of LL-1 in the biosynthesis of steroids pathway. Two pathway members, ERG11 and ERG2, that increase each other upon knockout, have the exact same effect on all their common targets, down-regulating 110 genes (orange rectangle) and up-regulating 308 genes (green rectangle).