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Passing messages between biological networks to refine predicted interactions.

ABSTRACT: Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.

SUBMITTER: Glass K

PROVIDER: S-EPMC3669401 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Passing messages between biological networks to refine predicted interactions.

Glass Kimberly K Huttenhower Curtis C Quackenbush John J Yuan Guo-Cheng GC

PloS one 20130531 5

Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regu ...[more]

PMID: 23741402

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Project description:Neurobiological systems rely on hierarchical and modular architectures to carry out intricate computations using minimal resources. A prerequisite for such systems to operate adequately is the capability to reliably and efficiently transfer information across multiple modules. Here, we study the features enabling a robust transfer of stimulus representations in modular networks of spiking neurons, tuned to operate in a balanced regime. To capitalize on the complex, transient dynamics that such networks exhibit during active processing, we apply reservoir computing principles and probe the systems' computational efficacy with specific tasks. Focusing on the comparison of random feed-forward connectivity and biologically inspired topographic maps, we find that, in a sequential set-up, structured projections between the modules are strictly necessary for information to propagate accurately to deeper modules. Such mappings not only improve computational performance and efficiency, they also reduce response variability, increase robustness against interference effects, and boost memory capacity. We further investigate how information from two separate input streams is integrated and demonstrate that it is more advantageous to perform non-linear computations on the input locally, within a given module, and subsequently transfer the result downstream, rather than transferring intermediate information and performing the computation downstream. Depending on how information is integrated early on in the system, the networks achieve similar task-performance using different strategies, indicating that the dimensionality of the neural responses does not necessarily correlate with nonlinear integration, as predicted by previous studies. These findings highlight a key role of topographic maps in supporting fast, robust, and accurate neural communication over longer distances. Given the prevalence of such structural feature, particularly in the sensory systems, elucidating their functional purpose remains an important challenge toward which this work provides relevant, new insights. At the same time, these results shed new light on important requirements for designing functional hierarchical spiking networks.

Project description:BackgroundSeveral studies have demonstrated that synthetic lethal genetic interactions between gene mutations provide an indication of functional redundancy between molecular complexes and pathways. These observations help explain the finding that organisms are able to tolerate single gene deletions for a large majority of genes. For example, system-wide gene knockout/knockdown studies in S. cerevisiae and C. elegans revealed non-viable phenotypes for a mere 18% and 10% of the genome, respectively. It has been postulated that the low percentage of essential genes reflects the extensive amount of genetic buffering that occurs within genomes. Consistent with this hypothesis, systematic double-knockout screens in S. cerevisiae and C. elegans show that, on average, 0.5% of tested gene pairs are synthetic sick or synthetic lethal. While knowledge of synthetic lethal interactions provides valuable insight into molecular functionality, testing all combinations of gene pairs represents a daunting task for molecular biologists, as the combinatorial nature of these relationships imposes a large experimental burden. Still, the task of mapping pairwise interactions between genes is essential to discovering functional relationships between molecular complexes and pathways, as they form the basis of genetic robustness. Towards the goal of alleviating the experimental workload, computational techniques that accurately predict genetic interactions can potentially aid in targeting the most likely candidate interactions. Building on previous studies that analyzed properties of network topology to predict genetic interactions, we apply random walks on biological networks to accurately predict pairwise genetic interactions. Furthermore, we incorporate all published non-interactions into our algorithm for measuring the topological relatedness between two genes. We apply our method to S. cerevisiae and C. elegans datasets and, using a decision tree classifier, integrate diverse biological networks and show that our method outperforms established methods.ResultsBy applying random walks on biological networks, we were able to predict synthetic lethal interactions at a true positive rate of 95 percent against a false positive rate of 10 percent in S. cerevisiae. Similarly, in C. elegans, we achieved a true positive rate of 95 against a false positive rate of 7 percent. Furthermore, we demonstrate that the inclusion of non-interacting gene pairs results in a considerable performance improvement.ConclusionWe presented a method based on random walks that accurately captures aspects of network topology towards the goal of classifying potential genetic interactions as either synthetic lethal or non-interacting. Our method, which is generalizable to all types of biological networks, is likely to perform well with limited information, as estimated by holding out large portions of the synthetic lethal interactions and non-interactions.

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Passing messages between biological networks to refine predicted interactions.

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Passing messages between biological networks to refine predicted interactions.

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