Yeast genetic map, thecellmap.org

http://thecellmap.org/costanzo2016/

Three zip files

-rw-r--r--@  1 hqin  staff   497M Jun 26 09:58 Raw genetic interaction datasets- Pair-wise interaction format.zip

-rw-r--r--@  1 hqin  staff    34M Jun 26 09:58 Raw genetic interaction datasets- Matrix format.zip

-rw-r--r--@  1 hqin  staff   147M Jun 26 09:59 Genetic interaction profile similarity matrices.zip

Expand to three folders

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. 


Reference
http://hongqinlab.blogspot.com/2013/06/notes-costanzo-sga-2009.html


20180131Wed

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.