Two genes in an organism have a Synthetic Sickness Lethality (SSL)
interaction, if their joint deletion leads to a lower than
expected fitness. Synthetic Gene Array (SGA) is a technique that
helps in identifying SSL values for pairs of genes in a given set of
genes. SSL interactions are useful to discover the co-expressed
gene groups in the regulatory and signaling networks. Also, they are
used to unravel the pair of pathways (subset of physically
interacting genes) that substitute the functions of each other.
Generating an SGA entry is costly as it requires producing and
monitoring a double mutant (a progeny with two mutated genes).
Generating a comprehensive SGA can be very expensive as the number
of gene pairs is quadratic in the number of genes of the
In this paper, we develop a new method SSLPred to predict the
SSL interactions in an organism. Our method is built on the concept
of Between Pathway Models (BPM), where majority of the SSL
pairs span across the two functionally complementing pathways. We
develop a regression based approach that learns the mapping between
the gene expressions of single deletion mutant to the corresponding
SGA entries. We compare our method to the one by Hescott et al. for
predicting the GI (Genetic Interaction) score of Saccharomyces
cerevisiae on four benchmark datasets. On
different experimental setups, on average SSLPred performs
significantly better compared to the other method.