Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL Datasets

<p>Abstract</p> <p>Background</p> <p>The combination of genotypic and genome-wide expression data arising from segregating populations offers an unprecedented opportunity to model and dissect complex phenotypes. The immense potential offered by these data derives from the fact that genotypic variation is the sole source of perturbation and can therefore be used to reconcile changes in gene expression programs with the parental genotypes. To date, several methodologies have been developed for modeling eQTL data. These methods generally leverage genotypic data to resolve causal relationships among gene pairs implicated as associates in the expression data. In particular, leading studies have augmented Bayesian networks with genotypic data, providing a powerful framework for learning and modeling causal relationships. While these initial efforts have provided promising results, one major drawback associated with these methods is that they are generally limited to resolving causal orderings for transcripts most proximal to the genomic loci. In this manuscript, we present a probabilistic method capable of learning the causal relationships between transcripts at all levels in the network. We use the information provided by our method as a prior for Bayesian network structure learning, resulting in enhanced performance for gene network reconstruction.</p> <p>Results</p> <p>Using established protocols to synthesize eQTL networks and corresponding data, we show that our method achieves improved performance over existing leading methods. For the goal of gene network reconstruction, our method achieves improvements in recall ranging from 20% to 90% across a broad range of precision levels and for datasets of varying sample sizes. Additionally, we show that the learned networks can be utilized for expression quantitative trait loci mapping, resulting in upwards of 10-fold increases in recall over traditional univariate mapping.</p> <p>Conclusions</p> <p>Using the information from our method as a prior for Bayesian network structure learning yields large improvements in accuracy for the tasks of gene network reconstruction and expression quantitative trait loci mapping. In particular, our method is effective for establishing causal relationships between transcripts located both proximally and distally from genomic loci.</p

Predicting genetic interactions with random walks on biological networks

Abstract Background Several 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. Results By 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. Conclusion We 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.</p

Handedness of a Motor Program in <em>C. elegans</em> Is Independent of Left-Right Body Asymmetry

<div><p>Complex animals display bilaterally asymmetric motor behavior, or “motor handedness,” often revealed by preferential use of limbs on one side. For example, use of right limbs is dominant in a strong majority of humans. While the mechanisms that establish bilateral asymmetry in motor function are unknown in humans, they appear to be distinct from those for other handedness asymmetries, including bilateral visceral organ asymmetry, brain laterality, and ocular dominance. We report here that a simple, genetically homogeneous animal comprised of only ∼1000 somatic cells, the nematode <em>C. elegans</em>, also shows a distinct motor handedness preference: on a population basis, males show a pronounced right-hand turning bias during mating. The handedness bias persists through much of adult lifespan, suggesting that, as in more complex animals, it is an intrinsic trait of each individual, which can differ from the population mean. Our observations imply that the laterality of motor handedness preference in <em>C. elegans</em> is driven by epigenetic factors rather than by genetic variation. The preference for right-hand turns is also seen in animals with mirror-reversed anatomical handedness and is not attributable to stochastic asymmetric loss of male sensory rays that occurs by programmed cell death. As with <em>C. elegans</em>, we also observed a substantial handedness bias, though not necessarily the same preference in direction, in several gonochoristic <em>Caenorhabditis</em> species. These findings indicate that the independence of bilaterally asymmetric motor dominance from overall anatomical asymmetry, and a population-level tendency away from ambidexterity, occur even in simple invertebrates, suggesting that these may be common features of bilaterian metazoans.</p> </div

Persistence of handedness preference over two days of adulthood for N2.

<p>(<b>A</b>) and <i>gpa-16(-)</i> animals (<b>B</b>). Symbols on the left indicate Day 1 HBVs, symbols on the right indicate Day 2 HBVs for each worm scored. Plotting the rank of the HBVs reveals significant consistency in behavior over a two-day period for (<b>C</b>) N2 and (<b>D</b>) <i>gpa-16(-)</i> worms.</p

Left-right male turning behavior during mating.

<p>(<b>A</b>) Right turn (here, a difficult “under” turn). The male is lying on its right side and turning right, causing it to pass underneath the hermaphrodite. (<b>B</b>) Left turn (here, an easy “over” turn). The male is lying on its right side and turning towards its left to pass over the hermaphrodite. Arrows indicate points where the male’s tail passes over or under the hermaphrodite's body.</p

Motor handedness bias of five <i>Caenorhabditis</i> species.

<p>(<b>A</b>) HBVs of individual worms for N2 (n = 32), <i>C. briggsae</i> (n = 23), <i>C. japonica</i> (n = 19), <i>C. remanei</i> (n = 19) and <i>C. brenneri</i> (n = 23) samples. (<b>B</b>) Log (p-value of two-tailed binomial test) of the same worms as in (A) and plotted as in Fig. 4. (<b>C</b>) Log transformation of the p-values representing binomial logistic regression model fits for the indicated species. (<b>D</b>) Estimates of the binomial logistic regression π parameter for all 9 samples used in this study. There are 10 possible pairwise comparisons between the 5 N2-related strains; only one was marginally significantly different at the 0.05 threshold (<i>spe-12</i> vs. <i>gpa-16</i> reversed; p = 0.047). By contrast, all 5 N2-related strains are significantly different from each of the other 4 <i>Caenorhabditis</i> species (20 possible pairwise comparisons).</p

The wild-type (N2) <i>C. elegans</i> male population is predominantly right-handed.

<p>(<b>A</b>) HBV distribution of individual N2 worms (n = 32). (<b>B</b>) Plot of the log(p-value, two-tailed binomial test) for the data shown in (A). Right-handed worms are plotted with -1*log(p-value), whereas worms making predominantly left-handed turns are plotted with +1*log(p-value). Dashed lines represent log(p = 0.05). A majority of N2 worms scored were right-biased, and 10 were significant at the 0.05 threshold. (<b>C</b>) HBV for the N2 data partitioned based on orientation, which is demonstrably a significant factor in influencing turning behavior. (<b>D</b>) Plotting the ranks of the HBVs on the partitioned data reveals a significant correlation, indicating that individual biases in handedness are consistent across sides.</p

Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network

Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm GRN. While some natural isolates show a nearly absolute requirement for these two regulators, in others, most embryos differentiate endoderm in their absence. GWAS and analysis of recombinant inbred lines reveal multiple genetic regions underlying this broad phenotypic variation. We observe a reciprocal trend, in which genomic variants, or knockdown of endoderm regulatory genes, that result in a high SKN-1 requirement often show low MOM-2/Wnt requirement and vice-versa, suggesting that cryptic variation in the endoderm GRN may be tuned by opposing requirements for these two key regulatory inputs. These findings reveal that while the downstream components in the endoderm GRN are common across metazoan phylogeny, initiating regulatory inputs are remarkably plastic even within a single species