I study computational and quantitative biology with a focus on network aging. This site is to serve as my note-book and to effectively communicate with my students and collaborators. Every now and then, a blog may be of interests to other researchers or teachers. Views in this blog are my own. All rights of research results and findings on this blog are reserved. See also http://youtube.com/c/hongqin
drwxr-xr-x@ 7 hqin staff 238B Dec 6 2016 Data File S1. Raw genetic interaction datasets: Pair-wise interaction format
drwxr-xr-x@ 18 hqin staff 612B Dec 6 2016 Data File S2. Raw genetic interaction datasets: Matrix format
drwxr-xr-x@ 5 hqin staff 170B Oct 20 2016 Data File S3. Genetic interaction profile similarity matrices
The global interaction dataset is based on the construction and analysis of ~23 million double mutants which identified 550,000 negative and 350,000 positive genetic interactions and covers ~90% of all yeast genes as either array and/or query mutants. The global genetic interaction dataset includes three different genetic interaction maps. First, 3,589 nonessential deletion query mutant strains were screened against the deletion mutant array covering 3,892 nonessential genes to generate a nonessential x nonessential (NxN) network. Second, 1,162 TS query mutant strains representing 804 essential genes were also screened against the nonessential deletion mutant array to generate an essential x nonessential (ExN) network. Finally, 2,241 nonessential deletion mutant query strains and 1,108 TS query mutant strains, corresponding to 795 essential genes, were crossed to an array of 792 TS strains, spanning 561 unique essential genes, to generate an expanded ExN network and an essential x essential (ExE) network. The data can be downloaded from the links below. Note that we continue to map genetic interactions for remaining gene pairs not represented in this dataset and we will update the data and networks as new interactions are generated.
Correction: e should be epsilon. abs(epsilon)>0.08 should be used for intermediate criteria.
No self-interactions have been found in the cellmap network (using the stringent criteria). Therefore, to prepare the networks for permutation, I ordered all gene pairs alphabetically (i.e., both [A,B] and [B,A] will be changed to [A,B]), and then removed the redundant pairs (i.e., only one [A,B] was left).
However, after that I found that there are 878,704 overall interactions (both positive and negative), 540,396 negative interactions and 353,117 positive interactions.
Now the problem is that, neg + pos - all ~ 100k ... i.e., there are ~100k interactions have been found in both negative and positive sets.