Genomic data integration is a key goal to be achieved towards large-scale genomic data analysis. This process is very challenging due to the diverse sources of information resulting from genomics experiments. In this work, we review methods designed to combine genomic data recorded from microarray gene expression (MAGE) experiments. It has been acknowledged that the main source of variation between different MAGE datasets is due to the so-called 'batch effects'. The methods reviewed here perform data integration by removing (or more precisely attempting to remove) the unwanted variation associated with batch effects. They are presented in a unified framework together with a wide range of evaluation tools, which are mandatory in assessing the efficiency and the quality of the data integration process. We provide a systematic description of the MAGE data integration methodology together with some basic recommendation to help the users in choosing the appropriate tools to integrate MAGE data for large-scale analysis; and also how to evaluate them from different perspectives in order to quantify their efficiency. All genomic data used in this study for illustration purposes were retrieved from InSilicoDB http://insilico.ulb.ac.be.
A plenitude of feature selection (FS) methods is available in the literature, most of them rising as a need to analyze data of very high dimension, usually hundreds or thousands of variables. Such data sets are now available in various application areas like combinatorial chemistry, text mining, multivariate imaging, or bioinformatics. As a general accepted rule, these methods are grouped in filters, wrappers, and embedded methods. More recently, a new group of methods has been added in the general framework of FS: ensemble techniques. The focus in this survey is on filter feature selection methods for informative feature discovery in gene expression microarray (GEM) analysis, which is also known as differentially expressed genes (DEGs) discovery, gene prioritization, or biomarker discovery. We present them in a unified framework, using standardized notations in order to reveal their technical details and to highlight their common characteristics as well as their particularities.
In this work, we introduce a prebiotically relevant protometabolic pattern corresponding to an engine of deracemization by using an external energy source. The spontaneous formation of a nonracemic mixture of chiral compounds can be observed in out-ofequilibrium systems via a symmetry-breaking phenomenon. This observation is possible thanks to chirally selective autocatalytic reactions (Frank's model) [Frank, F. C. (1953) Biochim. Biophys. Acta 11, 459 -463]. We show that the use of a Frank-like model in a recycled system composed of reversible chemical reactions, rather than the classical irreversible system, allows for the emergence of a synergetic autoinduction from simple reactions, without any autocatalytic or even catalytic reaction. This model is described as a theoretical framework, based on the stereoselective reactivity of preexisting chiral monomeric building blocks (polymerization, epimerization, and depolymerization) maintained out of equilibrium by a continuous energy income, via an activation reaction. It permits the self-conversion of all monomeric subunits into a single chiral configuration. Real prebiotic systems of amino acid derivatives can be described on this basis. They are shown to be able to spontaneously reach a stable nonracemic state in a few centuries. In such systems, the presence of epimerization reactions is no more destructive, but in contrast is the central driving force of the unstabilization of the racemic state.prebiotic chemistry ͉ protometabolism T he emergence of homochirality is a crucial enigma in the origin of life (1): fundamental biomolecules are different from their mirror images and exist only in either the righthanded or left-handed form. For symmetry reasons, the first chiral prebiotic molecules should have been synthesized in equal amounts of both forms (2), but an initial enantiomeric excess of low value can easily exist (3), thanks to statistical fluctuation (4), asymmetry of weak forces (5), or induction by an asymmetric environment (6-9). The problem thus comes down to understanding how amplification phenomena could take place to enhance such initial deviance from symmetry, constituting a real symmetry breaking toward homochirality. Some explanations based on stereoselective polymerization are classically suggested (10, 11). However, the effect is only proportional to the initial excess and is to be destroyed in the long term by epimerization, so that these models are not sufficient as the racemic state remains stable (12).True symmetry breaking can occur in an dynamical out-ofequilibrium chemical system, as first introduced by Frank (13), allowing the destabilization of the racemic state. Several experimental systems corresponding to such a model have been described (14-18), but as Blackmond (19) recently concluded in an analysis about such experimental models, there is still a need of ''other organic transformations that could provide a closer model for how asymmetric amplification in the prebiotic world could have occurred.'' To be effective, such systems ...
Since the model proposed by Frank (Frank FC, Biochem Biophys Acta 1953;11:459-463), several alternative models have been developed to explain how an asymmetric non-racemic steady state can be reached by a chirally symmetric chemical reactive system. This paper explains how a stable non-racemic regime can be obtained as a symmetry breaking occurring in a far-from-equilibrium reactive system initiated with an initial imbalance. Departing from the variations around the original Frank's model that are commonly described in the literature, i.e. open-flow systems of direct autocatalytic reactions, we discuss recent developments emphasizing both an active recycling of components and an autocatalytic network of simple reactions. We will present our APED model as the most natural realization of such thermodynamic openness and non-equilibrium, of recycling and of network autocatalysis, each of these in prebiotic conditions. The different experimental and theoretical models in the literature will be classified according to mechanism. The place and role of such self-structured networks responsible for the presence of homochirality in the primitive Earth will be detailed.
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