A statistical framework for testing functional categories in microarray data

Ready access to emerging databases of gene annotation and functional pathways has shifted assessments of differential expression in DNA microarray studies from single genes to groups of genes with shared biological function. This paper takes a critical look at existing methods for assessing the differential expression of a group of genes (functional category), and provides some suggestions for improved performance. We begin by presenting a general framework, in which the set of genes in a functional category is compared to the complementary set of genes on the array. The framework includes tests for overrepresentation of a category within a list of significant genes, and methods that consider continuous measures of differential expression. Existing tests are divided into two classes. Class 1 tests assume gene-specific measures of differential expression are independent, despite overwhelming evidence of positive correlation. Analytic and simulated results are presented that demonstrate Class 1 tests are strongly anti-conservative in practice. Class 2 tests account for gene correlation, typically through array permutation that by construction has proper Type I error control for the induced null. However, both Class 1 and Class 2 tests use a null hypothesis that all genes have the same degree of differential expression. We introduce a more sensible and general (Class 3) null under which the profile of differential expression is the same within the category and complement. Under this broader null, Class 2 tests are shown to be conservative. We propose standard bootstrap methods for testing against the Class 3 null and demonstrate they provide valid Type I error control and more power than array permutation in simulated datasets and real microarray experiments.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS146 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Penyeimbangan Lingkungan Akibat Pencemaran Karbon yang Ditimbulkan Industri Warung Internet di Kota Pekanbaru

Penelitian ini dilakukan di Kota Pekanbaru, bertujuan untuk mengukur kebutuhan pohon yang perlu ditanam untuk menyeimbangkan lingkungan akibat pencemaran karbondioksida yang ditimbulkan oleh aktivitas industry warung internet (warnet), khususnya penyalaan komputer di warnet-warnet pada 3 kecamatan yang dijadikan sampel, Kecamatan Tampan, Kecamatan Sukajadi, dan Kecamatan Tenayan Raya. Dari penelitian terdahulu diketahui bahwa penyalaan komputer selama 100 jam akan menghasilkan emisi karbondioksida sebanyak 9 kg. Hasil analisis menemukan bahwa untuk menyeimbangkan lingkungan akibat pencemaran karbon dari industry warnet ini memerlukan penanaman sebanyak 24 pohon Trembesi di Kecamatan Tampan, 12 pohon Trembesi di Kecamatan Sukajadi, dan 4 pohon Trembesi di Kecamatan Tenayan Raya

High temperature mobility of CdTe

The Hall mobility of electrons μH is measured in CdTe in the temperature interval 450-1050°C and defined Cd overpressure in near-intrinsic conditions. The strong decrease of μH above 600°C is reported. The effect is explained within a model of multivalley conduction where both electrons in �1c minimum and in L1c minima participate. The theoretical description is based on the solution of the Boltzmann transport equation within the relaxation time approximation including the polar and acoustic phonon intravalley and intervalley scatterings. The �1c to L1c separation �E=0.29 - 10-4T (eV) for the effective mass in the L valley mL=0.35m0 is found to best fit the experimental data. Such �E is about four times smaller than it is predicted by first-principle calculations. © 2001 American Institute of Physics

Ergodicity, Decisions, and Partial Information

In the simplest sequential decision problem for an ergodic stochastic process X, at each time n a decision u_n is made as a function of past observations X_0,...,X_{n-1}, and a loss l(u_n,X_n) is incurred. In this setting, it is known that one may choose (under a mild integrability assumption) a decision strategy whose pathwise time-average loss is asymptotically smaller than that of any other strategy. The corresponding problem in the case of partial information proves to be much more delicate, however: if the process X is not observable, but decisions must be based on the observation of a different process Y, the existence of pathwise optimal strategies is not guaranteed. The aim of this paper is to exhibit connections between pathwise optimal strategies and notions from ergodic theory. The sequential decision problem is developed in the general setting of an ergodic dynamical system (\Omega,B,P,T) with partial information Y\subseteq B. The existence of pathwise optimal strategies grounded in two basic properties: the conditional ergodic theory of the dynamical system, and the complexity of the loss function. When the loss function is not too complex, a general sufficient condition for the existence of pathwise optimal strategies is that the dynamical system is a conditional K-automorphism relative to the past observations \bigvee_n T^n Y. If the conditional ergodicity assumption is strengthened, the complexity assumption can be weakened. Several examples demonstrate the interplay between complexity and ergodicity, which does not arise in the case of full information. Our results also yield a decision-theoretic characterization of weak mixing in ergodic theory, and establish pathwise optimality of ergodic nonlinear filters.Comment: 45 page

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

Background Analysis of microarray experiments often involves testing for the overrepresentation of pre-defined sets of genes among lists of genes deemed individually significant. Most popular gene set testing methods assume the independence of genes within each set, an assumption that is seriously violated, as extensive correlation between genes is a well-documented phenomenon. Results We conducted a meta-analysis of over 200 datasets from the Gene Expression Omnibus in order to demonstrate the practical impact of strong gene correlation patterns that are highly consistent across experiments. We show that a common independence assumption-based gene set testing procedure produces very high false positive rates when applied to data sets for which treatment groups have been randomized, and that gene sets with high internal correlation are more likely to be declared significant. A reanalysis of the same datasets using an array resampling approach properly controls false positive rates, leading to more parsimonious and high-confidence gene set findings, which should facilitate pathway-based interpretation of the microarray data. Conclusions These findings call into question many of the gene set testing results in the literature and argue strongly for the adoption of resampling based gene set testing criteria in the peer reviewed biomedical literature

Vulnerability to xylem cavitation and the distribution of sonoran desert vegetation

Journal ArticleWe studied 15 riparian and upland Sonoran desert species to evaluate how the limitation of xylem pressure (Vx) by cavitation corresponded with plant distribution along a moisture gradient. Riparian species were obligate riparian trees (Fraxinus velutina, Populus fremontii, and Salix gooddingii), native shrubs (Baccharis spp.), and an exotic shrub (Tamarix ramosissima). Upland species were evergreen (Juniperus monosperma, Larrea tridentata), drought-deciduous (Ambrosia dumosa, Encelia farinosa, Fouquieria splendens, Cercidium microphyllum), and winter-deciduous (Acacia spp., Prosopis velutina) trees and shrubs

Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae

Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.Jennifer R. Bellon, Frank Schmid, Dimitra L. Capone, Barbara L. Dunn, Paul J. Chamber

The PKC, HOG and Ca2+ signalling pathways co-ordinately regulate chitin synthesis in Candida albicans

Open Access via PMC2649417Peer reviewedPublisher PD