Derivation of genetic interaction networks from quantitative phenotype data.
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ABSTRACT:
SUBMITTER: Drees BL
PROVIDER: S-EPMC1088966 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: A genetic interaction refers to the deviation of phenotypes from the expected when perturbing two genes simultaneously. Studying genetic interactions help clarify relationships between genes, such as compensation and masking, and identify gene groups of functional modules. Recently, several genome-scale experiments for measuring quantitative (positive and negative) genetic interactions have been conducted. The results revealed that genes in the same module usually interact with each other in a consistent way (pure positive or negative); this phenomenon was designated as monochromaticity. Monochromaticity might be the underlying principle that can be utilized to unveil the modularity of cellular networks. However, no appropriate quantitative measurement for this phenomenon has been proposed. RESULTS: In this study, we propose the monochromatic index (MCI), which is able to quantitatively evaluate the monochromaticity of potential functional modules of genes, and the MCI was used to study genetic landscapes in different cellular subsystems. We demonstrated that MCI not only amend the deficiencies of MP-score but also properly incorporate the background effect. The results showed that not only within-complex but also between-complex connections present significant monochromatic tendency. Furthermore, we also found that significantly higher proportion of protein complexes are connected by negative genetic interactions in metabolic network, while transcription and translation system adopts relatively even number of positive and negative genetic interactions to link protein complexes. CONCLUSION: In summary, we demonstrate that MCI improves deficiencies suffered by MP-score, and can be used to evaluate monochromaticity in a quantitative manner. In addition, it also helps to unveil features of genetic landscapes in different cellular subsystems. Moreover, MCI can be easily applied to data produced by different types of genetic interaction methodologies such as Synthetic Genetic Array (SGA), and epistatic miniarray profile (E-MAP).
| S-EPMC3278832 | biostudies-literature
Project description:High-throughput quantitative genetic interaction (GI) measurements provide detailed information regarding the structure of the underlying biological pathways by reporting on functional dependencies between genes. However, the analytical tools for fully exploiting such information lag behind the ability to collect these data. We present a novel Bayesian learning method that uses quantitative phenotypes of double knockout organisms to automatically reconstruct detailed pathway structures. We applied our method to a recent data set that measures GIs for endoplasmic reticulum (ER) genes, using the unfolded protein response as a quantitative phenotype. The results provided reconstructions of known functional pathways including N-linked glycosylation and ER-associated protein degradation. It also contained novel relationships, such as the placement of SGT2 in the tail-anchored biogenesis pathway, a finding that we experimentally validated. Our approach should be readily applicable to the next generation of quantitative GI data sets, as assays become available for additional phenotypes and eventually higher-level organisms.
| S-EPMC2913392 | biostudies-literature
Project description:Synthetic genetic arrays have been very effective at measuring genetic interactions in yeast in a high-throughput manner and recently have been expanded to measure quantitative changes in interaction, termed 'differential interactions', across multiple conditions. Here, we present a strategy that leverages statistical information from the experimental design to produce a novel, quantitative differential interaction score, which performs favorably compared to previous differential scores. We also discuss the added utility of differential genetic-similarity in differential network analysis. Our approach is preferred for differential network analysis, and our implementation, written in MATLAB, can be found at http://chianti.ucsd.edu/~gbean/compute_differential_scores.m.
| S-EPMC4056373 | biostudies-literature
Project description:A functionally diverse subset of yeast temperatures sensitive deletion mutants were transformed with a pool of barcoded yeast ORFs to identify dosage suppressors. Objective: To assess the relative strain proportion after growing DNA barcoded yeast deletion strains in a mixed pools. The barcodes are amplified from the mixed population, and the intensity of each labelled barcodes on the Tag4 array indicate the relative contribution of that strain to the mixed pool. Note: File MoBY_strains.txt available in E-TABM-1147.additional.zip
2012-04-21 | E-TABM-1147 | biostudies-arrayexpress
Project description:Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate proteins participating in the same molecular complex. Here, we propose a method for the joint learning of protein complexes and their functional relationships by integration of quantitative genetic interactions and TAP-MS data. Using 3 independent benchmark datasets, we demonstrate that this method is >50% more accurate at identifying functionally related protein pairs than previous approaches. Application to genes involved in yeast chromosome organization identifies a functional map of 91 multimeric complexes, a number of which are novel or have been substantially expanded by addition of new subunits. Interestingly, we find that complexes that are enriched for aggravating genetic interactions (i.e., synthetic lethality) are more likely to contain essential genes, linking each of these interactions to an underlying mechanism. These results demonstrate the importance of both large-scale genetic and physical interaction data in mapping pathway architecture and function.
| S-EPMC2289880 | biostudies-literature
Project description:Inferring regulatory and metabolic network models from quantitative genetic interaction data remains a major challenge in systems biology. Here, we present a novel quantitative model for interpreting epistasis within pathways responding to an external signal. The model provides the basis of an experimental method to determine the architecture of such pathways, and establishes a new set of rules to infer the order of genes within them. The method also allows the extraction of quantitative parameters enabling a new level of information to be added to genetic network models. It is applicable to any system where the impact of combinatorial loss-of-function mutations can be quantified with sufficient accuracy. We test the method by conducting a systematic analysis of a thoroughly characterized eukaryotic gene network, the galactose utilization pathway in Saccharomyces cerevisiae. For this purpose, we quantify the effects of single and double gene deletions on two phenotypic traits, fitness and reporter gene expression. We show that applying our method to fitness traits reveals the order of metabolic enzymes and the effects of accumulating metabolic intermediates. Conversely, the analysis of expression traits reveals the order of transcriptional regulatory genes, secondary regulatory signals and their relative strength. Strikingly, when the analyses of the two traits are combined, the method correctly infers ~80% of the known relationships without any false positives.
| S-EPMC3093353 | biostudies-literature
Project description:Over the past decade, biomedical research has witnessed an exponential increase in the throughput of the characterization of biological systems. Here we review the recent progress in large-scale methods to determine protein-protein, genetic and chemical-genetic interaction networks. We discuss some of the limitations and advantages of the different methods and give examples of how these networks are being used to study the evolutionary process. Comparative studies have revealed that different types of protein-protein interactions diverge at different rates with high conservation of co-complex membership but rapid divergence of more promiscuous interactions like those that mediate post-translational modifications. These evolutionary trends have consistent genetic consequences with highly conserved epistatic interactions within complex subunits but faster divergence of epistatic interactions across complexes or pathways. Finally, we discuss how these evolutionary observations are being used to interpret cross-species chemical-genetic studies and how they might shape therapeutic strategies. Together, these interaction networks offer us an unprecedented level of detail into how genotypes are translated to phenotypes, and we envision that they will be increasingly useful in the interpretation of genetic and phenotypic variation occurring within populations as well as the rational design of combinatorial therapeutics.
| S-EPMC3518490 | biostudies-literature
Project description:BackgroundControversy has attended the relationship between risk-adjusted mortality and process-of-care. There would be advantage in the establishment, at the data-base level, of global quantitative indices subsuming the diversity of process-of-care.MethodsA retrospective, cohort study of patients identified in the Australian and New Zealand Intensive Care Society Adult Patient Database, 1993-2003, at the level of geographic and ICU-level descriptors (n = 35), for both hospital survivors and non-survivors. Process-of-care indices were established by analysis of: (i) the smoothed time-hazard curve of individual patient discharge and determined by pharmaco-kinetic methods as area under the hazard-curve (AUC), reflecting the integrated experience of the discharge process, and time-to-peak-hazard (TMAX, in days), reflecting the time to maximum rate of hospital discharge; and (ii) individual patient ability to optimize output (as length-of-stay) for recorded data-base physiological inputs; estimated as a technical production-efficiency (TE, scaled [0,(maximum)1]), via the econometric technique of stochastic frontier analysis. For each descriptor, multivariate correlation-relationships between indices and summed mortality probability were determined.ResultsThe data-set consisted of 223129 patients from 99 ICUs with mean (SD) age and APACHE III score of 59.2(18.9) years and 52.7(30.6) respectively; 41.7% were female and 45.7% were mechanically ventilated within the first 24 hours post-admission. For survivors, AUC was maximal in rural and for-profit ICUs, whereas TMAX (>or= 7.8 days) and TE (>or= 0.74) were maximal in tertiary-ICUs. For non-survivors, AUC was maximal in tertiary-ICUs, but TMAX (>or= 4.2 days) and TE (>or= 0.69) were maximal in for-profit ICUs. Across descriptors, significant differences in indices were demonstrated (analysis-of-variance, P <or= 0.0001). Total explained variance, for survivors (0.89) and non-survivors (0.89), was maximized by combinations of indices demonstrating a low correlation with mortality probability.ConclusionsGlobal indices reflecting process of care may be formally established at the level of national patient data-bases. These indices appear orthogonal to mortality outcome.
| S-EPMC2873511 | biostudies-literature
Project description:The large volume of GWAS data poses great computational challenges for analyzing genetic interactions associated with common human diseases. We propose a computational framework for characterizing epistatic interactions among large sets of genetic attributes in GWAS data. We build the human phenotype network (HPN) and focus around a disease of interest. In this study, we use the GLAUGEN glaucoma GWAS dataset and apply the HPN as a biological knowledge-based filter to prioritize genetic variants. Then, we use the statistical epistasis network (SEN) to identify a significant connected network of pairwise epistatic interactions among the prioritized SNPs. These clearly highlight the complex genetic basis of glaucoma. Furthermore, we identify key SNPs by quantifying structural network characteristics. Through functional annotation of these key SNPs using Biofilter, a software accessing multiple publicly available human genetic data sources, we find supporting biomedical evidences linking glaucoma to an array of genetic diseases, proving our concept. We conclude by suggesting hypotheses for a better understanding of the disease.
| S-EPMC4299930 | biostudies-literature
Project description:Motivation: A central goal of current biology is to establish a complete functional link between the genotype and phenotype, known as the so-called genotype-phenotype map. With the continuous development of high-throughput technology and the decline in sequencing costs, multi-omics analysis has become more widely employed. While this gives us new opportunities to uncover the correlation mechanisms between single-nucleotide polymorphism (SNP), genes, and phenotypes, multi-omics still faces certain challenges, specifically: 1) When the sample size is large enough, the number of omics types is often not large enough to meet the requirements of multi-omics analysis; 2) each omics' internal correlations are often unclear, such as the correlation between genes in genomics; 3) when analyzing a large number of traits (p), the sample size (n) is often smaller than p, n << p, hindering the application of machine learning methods in the classification of disease outcomes. Results: To solve these issues with multi-omics and build a robust classification model, we propose a graph-embedded deep neural network (G-EDNN) based on expression quantitative trait loci (eQTL) data, which achieves sparse connectivity between network layers to prevent overfitting. The correlation within each omics is also considered such that the model more closely resembles biological reality. To verify the capabilities of this method, we conducted experimental analysis using the GSE28127 and GSE95496 data sets from the Gene Expression Omnibus (GEO) database, tested various neural network architectures, and used prior data for feature selection and graph embedding. Results show that the proposed method could achieve a high classification accuracy and easy-to-interpret feature selection. This method represents an extended application of genotype-phenotype association analysis in deep learning networks.
| S-EPMC9421127 | biostudies-literature