MetabR: an R script for linear model analysis of quantitative metabolomic data

Background Metabolomics is an emerging high-throughput approach to systems biology, but data analysis tools are lacking compared to other systems level disciplines such as transcriptomics and proteomics. Metabolomic data analysis requires a normalization step to remove systematic effects of confounding variables on metabolite measurements. Current tools may not correctly normalize every metabolite when the relationships between each metabolite quantity and fixed-effect confounding variables are different, or for the effects of random-effect confounding variables. Linear mixed models, an established methodology in the microarray literature, offer a standardized and flexible approach for removing the effects of fixed- and random-effect confounding variables from metabolomic data. Findings Here we present a simple menu-driven program, “MetabR”, designed to aid researchers with no programming background in statistical analysis of metabolomic data. Written in the open-source statistical programming language R, MetabR implements linear mixed models to normalize metabolomic data and analysis of variance (ANOVA) to test treatment differences. MetabR exports normalized data, checks statistical model assumptions, identifies differentially abundant metabolites, and produces output files to help with data interpretation. Example data are provided to illustrate normalization for common confounding variables and to demonstrate the utility of the MetabR program. Conclusions We developed MetabR as a simple and user-friendly tool for implementing linear mixed model-based normalization and statistical analysis of targeted metabolomic data, which helps to fill a lack of available data analysis tools in this field. The program, user guide, example data, and any future news or updates related to the program may be found at http://metabr.r-forge.r-project.org/ webcite

MetabR: an R script for linear model analysis of quantitative metabolomic data

Background Metabolomics is an emerging high-throughput approach to systems biology, but data analysis tools are lacking compared to other systems level disciplines such as transcriptomics and proteomics. Metabolomic data analysis requires a normalization step to remove systematic effects of confounding variables on metabolite measurements. Current tools may not correctly normalize every metabolite when the relationships between each metabolite quantity and fixed-effect confounding variables are different, or for the effects of random-effect confounding variables. Linear mixed models, an established methodology in the microarray literature, offer a standardized and flexible approach for removing the effects of fixed- and random-effect confounding variables from metabolomic data. Findings Here we present a simple menu-driven program, “MetabR”, designed to aid researchers with no programming background in statistical analysis of metabolomic data. Written in the open-source statistical programming language R, MetabR implements linear mixed models to normalize metabolomic data and analysis of variance (ANOVA) to test treatment differences. MetabR exports normalized data, checks statistical model assumptions, identifies differentially abundant metabolites, and produces output files to help with data interpretation. Example data are provided to illustrate normalization for common confounding variables and to demonstrate the utility of the MetabR program. Conclusions We developed MetabR as a simple and user-friendly tool for implementing linear mixed model-based normalization and statistical analysis of targeted metabolomic data, which helps to fill a lack of available data analysis tools in this field. The program, user guide, example data, and any future news or updates related to the program may be found at http://metabr.r-forge.r-project.org

Comparison of threshold selection methods for microarray gene co-expression matrices

<p>Abstract</p> <p>Background</p> <p>Network and clustering analyses of microarray co-expression correlation data often require application of a threshold to discard small correlations, thus reducing computational demands and decreasing the number of uninformative correlations. This study investigated threshold selection in the context of combinatorial network analysis of transcriptome data.</p> <p>Findings</p> <p>Six conceptually diverse methods - based on number of maximal cliques, correlation of control spots with expressed genes, top 1% of correlations, spectral graph clustering, Bonferroni correction of p-values, and statistical power - were used to estimate a correlation threshold for three time-series microarray datasets. The validity of thresholds was tested by comparison to thresholds derived from Gene Ontology information. Stability and reliability of the best methods were evaluated with block bootstrapping.</p> <p>Two threshold methods, number of maximal cliques and spectral graph, used information in the correlation matrix structure and performed well in terms of stability. Comparison to Gene Ontology found thresholds from number of maximal cliques extracted from a co-expression matrix were the most biologically valid. Approaches to improve both methods were suggested.</p> <p>Conclusion</p> <p>Threshold selection approaches based on network structure of gene relationships gave thresholds with greater relevance to curated biological relationships than approaches based on statistical pair-wise relationships.</p

Dynamic regulation of adipose tissue metabolism in the domestic broiler chicken – an alternative model for studies of human obesity

Background The domestic chicken is an attractive, but underutilized, animal model for studies of adipose tissue biology, metabolism and obesity: 1.) like humans, chickens rely on liver rather than adipose tissue for the majority of de novo lipogenesis; 2.) quantitative trait loci (QTLs) linked to fatness in chickens contain genes implicated in human susceptibility to obesity and diabetes; 3.) chickens are naturally hyperglycemic and insulin resistant; and 4.) a broad selection of genetic models exhibiting a range of fatness are available. To date, however, little is known about regulation of adipose metabolism in this model organism. Materials and methods Affymetrix arrays were used to profile gene expression in abdominal adipose tissue from broiler chickens fed ad libitum or fasted for five hours and from three distinct genetic lines with low (Fayoumi and Leghorn) or high (broiler) levels of adiposity. QPCR was used to validate microarray results for select genes. Western blotting was used to assay levels of signaling proteins. Tissue levels of beta-hydroxybutyrate were measured as an index of fatty acid oxidation using a colorimetric assay. Multiple testing was controlled using q-value. Mixed linear model and multivariate clustering analysis were implemented in SAS. The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (http://david.abcc.ncifcrf.gov/ webcite) was used for Gene Ontology (GO) and KEGG pathway enrichment analyses. Results A total of 1780 genes were differentially expressed in fasted vs. ad libitum fed (p\u3c0.05) tissue after correction for multiple testing. Gene Ontology and pathway analyses, combined with Western blot validation, indicated significant effects on a broad selection of pathways related to metabolism, stress signaling and adipogenesis. In particular, fasting upregulated rate-limiting genes in both the mitochondrial and peroxisomal pathways of beta-oxidation. Enhanced fatty acid oxidation in white adipose tissue was further suggested by a significant increase in tissue content of the ketone beta-hydroxybutyrate. Expression profiles suggested that, despite the relatively brief duration of feed withdrawal, fasting suppressed adipogenesis; expression of key genes in multiple steps of adipogenesis, including lineage commitment from mesenchymal stem cells, were significantly down-regulated in fasted vs. fed adipose tissue. Interestingly, fasting increased expression of several inflammatory adipokines and components of the toll-like receptor 4 signaling pathway. Microarray analysis of Fayoumi, Leghorn and broiler adipose tissue revealed that genetic leanness shared molecular signatures with the effects of fasting. In supervised clustering analysis, fasted broiler chickens clustered with lean Fayoumi and Leghorn lines rather than with the fed broiler group, suggesting that fasting manipulated expression profiles to resemble those of the lean phenotype. Conclusions Collectively, these data suggest that leanness in chickens is associated with increased fat utilization which, given the similarities between avian and human adipose tissue with regard to lipid metabolism, may have relevance for humans. The paradoxical increase in some inflammatory markers with an acute fast suggests that the dynamic relationship between inflammation and adipose metabolism may differ from what is observed in obesity. These results highlight chicken as a useful model in which to study the interrelationships between food intake, adipose development, metabolism, and cell stress

The Adipose Renin-Angiotensin System Modulates Systemic Markers of Insulin Sensitivity and Activates the Intrarenal Renin-Angiotensin System

Background. The adipose tissue renin-angiotensin system (RAS) contributes to regulation of fat mass and may also impact systemic functions such as blood pressure and metabolism. Methods and results. A panel of mouse models including mice lacking angiotensinogen, Agt (Agt-KO), mice expressing Agt solely in adipose tissue (aP2-Agt/Agt-KO), and mice overexpressing Agt in adipose tissue (aP2-Agt) was studied. Total body weight, epididymal fat pad weight, and circulating levels of leptin, insulin, and resistin were significantly decreased in Agt-KO mice, while plasma adiponectin levels were increased. aP2-Agt mice exhibited increased adiposity and plasma leptin and insulin levels compared to wild type (WT) controls. Angiotensinogen and type I Ang II receptor protein levels were also elevated in kidney of aP2-Agt mice. Conclusion. These findings demonstrate that alterations in adipose RAS activity significantly impact both local and systemic physiology in a way that may contribute to the detrimental health effects of obesity

Inferring gene coexpression networks for low dose ionizing radiation using graph theoretical algorithms and systems genetics

Background Biological data generated through large scale -omics technologies have resulted in a new paradigm in the study of biological systems. Instead of focusing on individual genes or proteins these technologies enable us to extract biological networks using powerful computing and statistical algorithms that are scalable to very large datasets. Materials and methods We have developed a tool chain using novel graph algorithms to extract gene coexpression networks from microarray data. We highlight implementation of our tool chain to investigate the effects of in vivo low dose ionizing radiation treatments on mice. We are using systems genetics approach to investigate the biological effects of low dose (10 cGy) ionizing radiation. We measured the base line gene expression profile from spleen tissue of BXD recombinant inbred mice using Illumina microarrays. The data was filtered using coefficient of variance after robust spline normalization and variance stabilizing transformation. A graph was then derived from this data, with probes as vertices and edges between them representing correlations. The graph was analyzed using our toolkit to find the size and number of maximal cliques. We deployed another tool called paraclique that relaxes clique’s requirement that every edge be present between all vertices. Paraclique enables us to account for inherent noise in the microarray data and stochastic nature of biological processes. Using immunophenotype data from the baseline BXD mice, we employed biclique analysis to determine interactions between genotypes and immunophenotypes (%CD4, %CD3, LN T:B, %CD8, and LN CD4:CD8). We also extracted eQTLs from BXD data using QTL-Reaper from base line gene expression profiles. 1881 transcripts were associated with 686 loci. The eQTLs were classified as cis or trans according to their genomic positions. Besides population level studies we also investigated the differential effect of low dose and high dose (1Gy) of ionizing radiations on spleen gene expression in inbred parental strains (C57BL/6J and DBA/2J) of BXD recombinant inbred mice as well as BALB/c mice, a known radiation-sensitive strain

Maternal consumption of fish oil programs reduced adiposity in broiler chicks

Maternal intake of eicosapentaenoic acid (EPA; 20:5 n-3) and docosahexaenoic acid (22:6 n-3) has been associated with reduced adiposity in children, suggesting the possibility to program adipose development through dietary fatty acids before birth. This study determined if enriching the maternal diet in fish oil, the primary source of EPA and DHA, affected adipose development in offspring. Broiler chickens were used because they are obesity-prone, and because fatty acids provided to the embryo can be manipulated through the hen diet. Hens were fed diets supplemented (2.8% wt:wt) with corn oil (CO; n-6) or fish oil (FO; n-3) for 28 d. Chicks from both maternal diet groups were fed the same diet after hatch. Maternal FO consumption enriched chick adipose tissue in EPA and DHA and reduced adiposity by promoting more, but smaller, adipocytes. This adipocyte profile was paralleled by upregulated expression of the adipogenic regulator PPARGand its co-activator PPARGC1B, and reduced expression of LPL. Proteomics identified 95 differentially abundant proteins between FO and CO adipose tissue, including components of glucose metabolism, lipid droplet trafficking, and cytoskeletal organization. These results demonstrate that the maternal dietary fatty acid profile programs offspring adipose development

Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms

Genes with common functions often exhibit correlated expression levels, which can be used to identify sets of interacting genes from microarray data. Microarrays typically measure expression across genomic space, creating a massive matrix of co-expression that must be mined to extract only the most relevant gene interactions. We describe a graph theoretical approach to extracting co-expressed sets of genes, based on the computation of cliques. Unlike the results of traditional clustering algorithms, cliques are not disjoint and allow genes to be assigned to multiple sets of interacting partners, consistent with biological reality. A graph is created by thresholding the correlation matrix to include only the correlations most likely to signify functional relationships. Cliques computed from the graph correspond to sets of genes for which significant edges are present between all members of the set, representing potential members of common or interacting pathways. Clique membership can be used to infer function about poorly annotated genes, based on the known functions of better-annotated genes with which they share clique membership (i.e., “guilt-by-association”). We illustrate our method by applying it to microarray data collected from the spleens of mice exposed to low-dose ionizing radiation. Differential analysis is used to identify sets of genes whose interactions are impacted by radiation exposure. The correlation graph is also queried independently of clique to extract edges that are impacted by radiation. We present several examples of multiple gene interactions that are altered by radiation exposure and thus represent potential molecular pathways that mediate the radiation response

A systematic comparison of genome-scale clustering algorithms

Background: A wealth of clustering algorithms has been applied to gene co-expression experiments. These algorithms cover a broad range of approaches, from conventional techniques such as k-means and hierarchical clustering, to graphical approaches such as k-clique communities, weighted gene co-expression networks (WGCNA) and paraclique. Comparison of these methods to evaluate their relative effectiveness provides guidance to algorithm selection, development and implementation. Most prior work on comparative clustering evaluation has focused on parametric methods. Graph theoretical methods are recent additions to the tool set for the global analysis and decomposition of microarray co-expression matrices that have not generally been included in earlier methodological comparisons. In the present study, a variety of parametric and graph theoretical clustering algorithms are compared using well-characterized transcriptomic data at a genome scale from Saccharomyces cerevisiae. Methods: For each clustering method under study, a variety of parameters were tested. Jaccard similarity was used to measure each clusters agreement with every GO and KEGG annotation set, and the highest Jaccard score was assigned to the cluster. Clusters were grouped into small, medium, and large bins, and the Jaccard score of the top five scoring clusters in each bin were averaged and reported as the best average top 5 (BAT5) score for the particular method. Results: Clusters produced by each method were evaluated based upon the positive match to known pathways. This produces a readily interpretable ranking of the relative effectiveness of clustering on the genes. Methods were also tested to determine whether they were able to identify clusters consistent with those identified by other clustering methods. Conclusions: Validation of clusters against known gene classifications demonstrate that for this data, graph-based techniques outperform conventional clustering approaches, suggesting that further development and application of combinatorial strategies is warranted

n3 and n6 polyunsaturated fatty acids differentially modulate prostaglandin E secretion but not markers of lipogenesis in adipocytes

A dramatic rise in the incidence of obesity in the U.S. has accelerated the search for interventions that may impact this epidemic. One recently recognized target for such intervention is adipose tissue, which secretes a variety of bioactive substances including prostaglandins. Prostaglandin E2 (PGE2) has been shown to decrease lipolysis in adipocytes, but limited studies have explored alternative mechanisms by which PGE2 might impact obesity, such as adipogenesis or lipogenesis. Studies conducted on ApcMin/+ mice indicated that selective inhibition of the cyclooxygenase (COX)-2 enzyme led to significant reductions in fatty acid synthase (FAS) activity in adipose tissue suggesting lipogenic effects of PGE2. To further investigate whether these lipid mediators directly regulate lipogenesis, we used 3T3-L1 adipocytes to determine the impact of eicosapentaenoic acid (EPA) and celecoxib on PGE2 formation and FAS used as a lipogenic marker. Both arachidonic acid (AA) and EPA dose-dependently increased PGE secretion from adipocytes. AA was expectedly more potent and exhibiting at 150 uM dose a 5-fold increase in PGE2 secretion over EPA. Despite higher secretion of PGE by EPA and AA compared to control, neither PUFA significantly altered FAS activity. By contrast both AA and EPA significantly decreased FAS mRNA levels. Addition of celecoxib, a selective COX-2 inhibitor, significantly decreased PGE2 secretion (p < 0.05) versus control, and also significantly decreased FAS activity (p < 0.05). Unexpectedly, the combination of exogenous PGE2 and celecoxib further decreased the FAS activity compared to PGE2 alone or untreated controls. In conclusion, EPA-mediated inhibition of AA metabolism did not significantly alter FAS activity while both AA and EPA significantly decreased FAS mRNA expression. COX-2 inhibition significantly decreased PGE2 production resulting in a decrease in FAS activity and expression that was not reversed with the addition of exogenous PGE2, suggesting an additional mechanism that is independent of COX-2