Towards accurate imputation of quantitative genetic interactions

Table 1 Features used in this study

Feature group	Characteristic	Number of features	Data source	Previous use for GI prediction
NETWORK	Physical interaction	1	BioGrid [28]	[13, 20]
	Shortest physical path	1	BioGrid [28]	[13, 20]
	Mutual clustering coefficient	1	BioGrid [28]	[13, 20]
	Network degree	6	BioGrid [28] and E-MAP	[20]
	2-hop	6	BioGrid [28] and the E-MAP	[13]
GENOMIC	Sequence similarity (BLAST E-value)	1	[45]	[13]
	Occurrence in a specific protein complex	32	MIPS [42]	-
	Co-occurrence in any protein complex	1	MIPS [42]	[13]
	Deletion phenotype	53	MIPS [42]	-
	A common deletion phenotype	1	MIPS [42]	[13]
	Correlation of quantitative phenotype profiles	1	[44]	-
	Gene Ontology semantic similarity	3	GO [58]	[13]
	Subcellular localization	17	[46]	-
	A common subcellular localization	1	[46]	[13]
	S-score in S. pombe	1	[11]	-
	mRNA expression (correlation)	7	[47–53]	[13]
GSG	S-score between A and genes similar to B (or vice versa)	10	E-MAP	-
GSG-MATRIX	S-scores among genes similar to A and to genes similar to B	25	E-MAP	-

The features are computed for every pair (A-B) of genes. Numbers of certain features depend on the E-MAP and are reported for the ChromBio E-MAP. SL, synthetic lethal; SS, synthetic sick.

ISSN: 1474-760X