Article

# A new class of bivariate copulas

Departamento de Estadı́stica y Matemática Aplicada, Universidad de Almerı́a, Carretera de Sacramento s/n 04120, La Cañada de San Urbano, Almerı́a, Spain

Statistics [?] Probability Letters (Impact Factor: 0.53). 01/2004; 66(3):315-325. DOI: 10.1016/j.spl.2003.09.010 - [Show abstract] [Hide abstract]

**ABSTRACT:**A multivariate distribution can be represented in terms of its underlying margins by binding these margins together using a copula function (Sklar, 1959). Here, we propose a new class of survival FGM-type modification truncated copulas which quantify dependency and incorporate directional dependence. In addition, we apply our proposed methods to the analysis of directional dependence relationships between genes. Finally, we employ the Akaike Information Criterion (AIC) to check the goodness of fit for our proposed copula models.Communication in Statistics- Simulation and Computation 01/2009; 38:1470-1484. · 0.30 Impact Factor - [Show abstract] [Hide abstract]

**ABSTRACT:**Background Genes interact with each other as basic building blocks of life, forming a complicated network. The relationship between groups of genes with different functions can be represented as gene networks. With the deposition of huge microarray data sets in public domains, study on gene networking is now possible. In recent years, there has been an increasing interest in the reconstruction of gene networks from gene expression data. Recent work includes linear models, Boolean network models, and Bayesian networks. Among them, Bayesian networks seem to be the most effective in constructing gene networks. A major problem with the Bayesian network approach is the excessive computational time. This problem is due to the interactive feature of the method that requires large search space. Since fitting a model by using the copulas does not require iterations, elicitation of the priors, and complicated calculations of posterior distributions, the need for reference to extensive search spaces can be eliminated leading to manageable computational affords. Bayesian network approach produces a discretely expression of conditional probabilities. Discreteness of the characteristics is not required in the copula approach which involves use of uniform representation of the continuous random variables. Our method is able to overcome the limitation of Bayesian network method for gene-gene interaction, i.e. information loss due to binary transformation. Results We analyzed the gene interactions for two gene data sets (one group is eight histone genes and the other group is 19 genes which include DNA polymerases, DNA helicase, type B cyclin genes, DNA primases, radiation sensitive genes, repaire related genes, replication protein A encoding gene, DNA replication initiation factor, securin gene, nucleosome assembly factor, and a subunit of the cohesin complex) by adopting a measure of directional dependence based on a copula function. We have compared our results with those from other methods in the literature. Although microarray results show a transcriptional co-regulation pattern and do not imply that the gene products are physically interactive, this tight genetic connection may suggest that each gene product has either direct or indirect connections between the other gene products. Indeed, recent comprehensive analysis of a protein interaction map revealed that those histone genes are physically connected with each other, supporting the results obtained by our method. Conclusion The results illustrate that our method can be an alternative to Bayesian networks in modeling gene interactions. One advantage of our approach is that dependence between genes is not assumed to be linear. Another advantage is that our approach can detect directional dependence. We expect that our study may help to design artificial drug candidates, which can block or activate biologically meaningful pathways. Moreover, our copula approach can be extended to investigate the effects of local environments on protein-protein interactions. The copula mutual information approach will help to propose the new variant of ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks): an algorithm for the reconstruction of gene regulatory networks. - [Show abstract] [Hide abstract]

**ABSTRACT:**Copulas have become a useful tool for the multivariate modelling in both stochastics and statistics. In this article, fundamental properties that allow the characterization of the dependence structure of families of the bivariate distributions defined by the copula are reviewed. Also, the importance of both the Gaussian copula and the Archimedean family is emphasized while some classes of copulas are described. The usefulness for modelling either discrete or continuous random couples is highlighted. The construction of first-order Markov regression models for non-Gaussian responses illustrates the application of the copula.Revista Colombiana de Estadistica 06/2009; 32(1):33-58. · 0.11 Impact Factor

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