title: Imputing and predicting quantitative genetic interactions in epistatic MAPs.
abstract: Mapping epistatic (or genetic) interactions has emerged as an important network biology approach for establishing functional relationships among genes and proteins. Epistasis networks are complementary to physical protein interaction networks, providing valuable insight into both the function of individual genes and the overall wiring of the cell. A high-throughput method termed "epistatic mini array profiles" (E-MAPs) was recently developed in yeast to quantify alleviating or aggravating interactions between gene pairs. The typical output of an E-MAP experiment is a large symmetric matrix of interaction scores. One problem with this data is the large amount of missing values - interactions that cannot be measured during the high-throughput process or whose measurements were discarded due to quality filtering steps. These missing values can reduce the effectiveness of some data analysis techniques and prevent the use of others. Here, we discuss one solution to this problem, imputation using nearest neighbors, and give practical examples of the use of a freely available implementation of this method.
authors.affiliation: School of Computer Science and Informatics, University College Dublin, Dublin, Ireland. colm.ryan@ucd.ie
authors.forename: Colm
authors.initials: C
authors.lastname: Ryan
authors.forename: Gerard
authors.initials: G
authors.lastname: Cagney
authors.forename: Nevan
authors.initials: N
authors.lastname: Krogan
authors.forename: Pádraig
authors.initials: P
authors.lastname: Cunningham
authors.forename: Derek
authors.initials: D
authors.lastname: Greene
mesh_terms: D004843:Epistasis, Genetic; D053263:Gene Regulatory Networks; D057166:High-Throughput Screening Assays; D008957:Models, Genetic; D011237:Predictive Value of Tests; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins