A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis

MOTIVATION: Cancer diagnosis is one of the most important emerging clinical applications of gene expression microarray technology. We are seeking to develop a computer system for powerful and reliable cancer diagnostic model creation based on microarray data. To keep a realistic perspective on clinical applications we focus on multicategory diagnosis. To equip the system with the optimum combination of classifier, gene selection and cross-validation methods, we performed a systematic and comprehensive evaluation of several major algorithms for multicategory classification, several gene selection methods, multiple ensemble classifier methods and two cross-validation designs using 11 datasets spanning 74 diagnostic categories and 41 cancer types and 12 normal tissue types. RESULTS: Multicategory support vector machines (MC-SVMs) are the most effective classifiers in performing accurate cancer diagnosis from gene expression data. The MC-SVM techniques by Crammer and Singer, Weston and Watkins and one-versus-rest were found to be the best methods in this domain. MC-SVMs outperform other popular machine learning algorithms, such as k-nearest neighbors, backpropagation and probabilistic neural networks, often to a remarkable degree. Gene selection techniques can significantly improve the classification performance of both MC-SVMs and other non-SVM learning algorithms. Ensemble classifiers do not generally improve performance of the best non-ensemble models. These results guided the construction of a software system GEMS (Gene Expression Model Selector) that automates high-quality model construction and enforces sound optimization and performance estimation procedures. This is the first such system to be informed by a rigorous comparative analysis of the available algorithms and datasets. AVAILABILITY: The software system GEMS is available for download from http://www.gems-system.org for non-commercial use. CONTACT: alexander.statnikov@vanderbilt.edu.     

Extraction of information on the buildup and consumption of reactive intermediates from quadruplex DNA assembly time courses

A method was developed to detect the time course of the overall presence of intermediate species during K+-induced DNA quadruplex assembly from single-stranded d(TG4) oligonucleotides in experiments in which only the combined circular dichroisms (CD) of all species present could be measured directly. The presence of intermediate species is determined unambiguously but quantitative estimates can be made only to the extent that the CD characteristics of all intermediates are known. The method consists of (i) obtaining CD spectra of known concentrations of initial and final species to determine their molar ellipticity coefficients, (ii) carrying out CD measurements of the kinetics of quadruplex assembly reactions at two different wavelengths, chosen to give optimal differentiation between the initial and final species, and (iii) using the results of (ii) to detect discrepancies between the rates of consumption of single strands and the generation of quadruplex to infer the presence of intermediate species. The analysis was facilitated by the validation and use of biphasic exponential expressions obtained from the SAS nonlinear curve fitting procedure NLIN in place of the raw CD data. The general method is described, then applied to data from [d(TG4)4.(K+)3] quadruplex assembly experiments.     

The F-BAR domain of SRGP-1 facilitates cell-cell adhesion during C. elegans morphogenesis

Robust cell-cell adhesion is critical for tissue integrity and morphogenesis, yet little is known about the molecular mechanisms controlling cell-cell junction architecture and strength. We discovered that SRGP-1 is a novel component of cell-cell junctions in Caenorhabditis elegans, localizing via its F-BAR (Bin1, Amphiphysin, and RVS167) domain and a flanking 200-amino acid sequence. SRGP-1 activity promotes an increase in membrane dynamics at nascent cell-cell contacts and the rapid formation of new junctions; in addition, srgp-1 loss of function is lethal in embryos with compromised cadherin-catenin complexes. Conversely, excess SRGP-1 activity leads to outward bending and projections of junctions. The C-terminal half of SRGP-1 interacts with the N-terminal F-BAR domain and negatively regulates its activity. Significantly, in vivo structure-function analysis establishes a role for the F-BAR domain in promoting rapid and robust cell adhesion during embryonic closure events, independent of the Rho guanosine triphosphatase-activating protein domain. These studies establish a new role for this conserved protein family in modulating cell-cell adhesion.     

Rapid epithelial-sheet sealing in the Caenorhabditis elegans embryo requires cadherin-dependent filopodial priming.

BACKGROUND: During embryonic development, epithelia with free edges must join together to create continuous tissues that seal the interior of the organism from the outside environment; failure of epithelial sealing underlies several common human birth defects. Sealing of epithelial sheets in embryos can be extremely rapid, dramatically exceeding the rate of adherens junction formation by epithelial cells in culture or during healing of epithelial wounds. Little is known about the dynamic redistribution of cellular junctional components during such events in living embryos. RESULTS: We have used time-lapse, multiphoton laser-scanning microscopy and green fluorescent protein fusion proteins to analyze the sealing of the Caenorhabditis elegans epidermis in living embryos. Rapid recruitment of alpha-catenin to sites of filopodial contact between contralateral migrating epithelial cells, concomitant with clearing of cytoplasmic alpha-catenin, resulted in formation of nascent junctions; this preceded the formation of mature junctions. Surprisingly, upon inactivation of the entire cadherin-catenin complex, only adhesive strengthening between filopodia was reproducibly affected. Other ventral epidermal cells, which did not extend filopodia and appeared to seal along the ventral midline by coordinated changes in cell shape, successfully adhered in the absence of these proteins. CONCLUSIONS: We propose that 'filopodial priming' - prealignment of bundled actin in filopodia combined with the rapid recruitment of alpha-catenin from cytoplasmic reserves at sites of filopodial contact - accounts for the rapid rate of sealing of the embryonic epidermis of C. elegans. Filopodial priming may provide a general mechanism for rapid creation of adherens junctions during epithelial-sheet sealing in embryos.