Sunday, February 25, 2018

Synthetical lethals in cellmap genetic networks



Guo: I think this is explained in the paper, van Leeuwen et al.,  "Exploring genetic suppression interactions on a global scale", Science (2016), 354:aag0839.

This paper mentioned synthetic letality but did not explicitly define if it is a positive or negative interaction. However, I think genetic interactions derived by synthetic lethality should be negative effect. As the positive effect indicates that if mutation of gene A causes a reduced fitness, the double mutation of A and B restored the fitness, and hence gene B is a genetic suppressor of gene A.

I cannot find it on the CellMap website. However, from the NxN database and the fitness data I identified 2191 negative GI's , in which the double mutant fitness (DMF) is lower than 0.1. You may use different criterion, e.g., 159 interactions with DMF <= 0; or 193 with DMF <= 0.01, etc.
See the attached csv file (ranked by the DMF). 

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