Emergent prop erties arise from hierarchical integration of the individual free copy components and organizational levels of complex systems, and, biologically, they are only manifest when the organ ism is considered in its entirety. Analogous to emergent properties in systems biology is the concept of latent vari ables in multivariate statistics. Latent variables are so called hidden variables generated in certain types of multivariate analysis which are not evident in original observed data. Rather, these latent variables emerge from consideration of the covar iance patterns when a large number of relevant variables are analyzed simultaneously. These latent variables may reflect a summarization of causal indicators underlying observed biological variability.

Given the parallelism between biological systems emergent properties and latent variables, we sought quite naturally to investigate the ability of latent variables to describe emergent properties, by applying multivariate analysis simultaneously to differ ent parts of a biological system, and notably to transcrip tional and post transcriptional data. Previously, successful parallel multi platform analyses were performed integrat ing genomic and transcriptional level, by using CGH arrays or SNPs and cDNA arrays. This approach portend to explain variations observed at the transcrip tional level, based on information at the genomic level. These approaches can annotate and map different types of probe IDs onto genomic coordinates, or add analyses at the translational level.

Brefeldin_A However, to date, simulta neous analysis of miRNA and mRNA from the same tissue have used only profile correlations. Herein, we expand analyses of molecular covariation beyond correlation of expression profiles by using the multivariate statistical pro cedure of multiple or common Factor Analysis. This procedure is widely used to reduce the dimensional ity of multivariate data and to do so in a manner that elu cidates the underlying or latent structure of the observed variation. Succinctly speaking, for a given set of molecular data, factor analysis partitions the observed pair wise cor relations between variables into that molecular covariation that is common between the variables from that which is unique to the individual variables. Application of FA directly on biological data without any a priori hypothesis about latent variables is ideal for data reduction. With this approach FA was used extensively to cluster microarray data. The use of the a priori knowledge on how each sample maps on tumor classes to constrain the rela tion between the latent variables under study and the fac tors obtained permits further data interpretation.