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PLoS One. 2018 Sep 12;13(9):e0203871. doi: 10.1371/journal.pone.0203871. eCollection 2018.

A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways.

Lu S1, Fan X1,2, Chen L1, Lu X1.

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Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
Department of Automation, Northwestern Polytechnical University, Shanxi, People's Republic of China.


Perturbing a signaling system with a serial of single gene deletions and then observing corresponding expression changes in model organisms, such as yeast, is an important and widely used experimental technique for studying signaling pathways. People have developed different computational methods to analyze the perturbation data from gene deletion experiments for exploring the signaling pathways. The most popular methods/techniques include K-means clustering and hierarchical clustering techniques, or combining the expression data with knowledge, such as protein-protein interactions (PPIs) or gene ontology (GO), to search for new pathways. However, these methods neither consider nor fully utilize the intrinsic relation between the perturbation of a pathway and expression changes of genes regulated by the pathway, which served as the main motivation for developing a new computational method in this study. In our new model, we first find gene transcriptomic modules such that genes in each module are highly likely to be regulated by a common signal. We then use the expression status of those modules as readouts of pathway perturbations to search for up-stream pathways. Systematic evaluation, such as through gene ontology enrichment analysis, has provided evidence that genes in each transcriptomic module are highly likely to be regulated by a common signal. The PPI density analysis and literature search revealed that our new perturbation modules are functionally coherent. For example, the literature search revealed that 9 genes in one of our perturbation module are related to cell cycle and all 10 genes in another perturbation module are related by DNA damage, with much evidence from the literature coming from in vitro or/and in vivo verifications. Hence, utilizing the intrinsic relation between the perturbation of a pathway and the expression changes of genes regulated by the pathway is a useful method of searching for signaling pathways using genetic perturbation data. This model would also be suitable for analyzing drug experiment data, such as the CMap data, for finding drugs that perturb the same pathways.

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