BioGRID-Costanzo2016.tab2.zip

BioGRID data set containing the 380,059 high confidence allele-specific interactions described above collapsed down to 326,790 gene interactions. These gene-based interactions contain corresponding alleles, scores and p-values in the notes. For each corresponding geneA-geneB interaction, the quantitative score from the highest scoring allele interaction for positive genetic interactions and lowest scoring one for negative genetic interactions is displayed in BioGRID and entered in column 19 of the download file. The other corresponding allele-specific interactions for each gene-based interaction are listed in the associated notes with their relevant scores and p-values. This data set does not include 21,039 merged/dubious ORFs present among the 380,059 interactions. Note that 1156 interactions had both positive and negative interactions for the same geneA-geneB interaction depending on the alleles used.

The file format and column headers are described here: https://wiki.thebiogrid.org/doku.php/biogrid_tab_version_2.0

Costanzo2016-HighestConfidence.tab.zip

Highest confidence data set of 380,059 allele-specific interactions. The raw dataset available at http://thecellmap.org/costanzo2016/ was first filtered for inconsistent reciprocal interactions as described above and then a stringent confidence threshold (p-value < 0.05 and SGA score< -0.12/SGA score> 0.16) was applied.

The tab-delimited file has 6 columns:

• 1.) Query Strain ID
• 2.) Query allele name
• 3.) Array Strain ID
• 4.) Array allele name
• 5.) Genetic interaction score (SGA score)
• 6.) P-value

Costanzo2016-Readme.txt

Readme for high throughput SGA data sets associated with the following publication:

Costanzo M, et al. "A global genetic interaction network maps a wiring diagram of cellular function." Science. 2016 Sep 23;353(6306). pii: aaf1420. PubMed PMID: 27708008.

Raw genetic interaction datasets- Pair-wise interaction format.zip

Full data set of 550,000 negative and 350,000 positive genetic interactions available as a raw dataset zip file posted here: http://thecellmap.org/costanzo2016/

Contains raw interaction data (SGA scores and p-values) for all tested pairs with one filter applied. For cases where reciprocal double mutant strains were constructed for the same pair of mutants (i.e. A-B and B-A), both pairs were filtered out if both interactions were significant and met the intermediate threshold (p-value < 0.05 and |score| > 0.08), but had opposite signs (e.g. A-B was negative and B-A was positive).

The tab-delimited file has 11 columns:

• 1.) Query Strain ID
• 2.) Query allele name
• 3.) Array Strain ID
• 4.) Array allele name
• 5.) Arraytype/Temp
• 6.) Genetic interaction score (e)
• 7.) P-value
• 8.) Query single mutant fitness (SMF)
• 9.) Array SMF
• 10.) Double mutant fitness
• 11.) Double mutant fitness standard deviation