A robust measure of correlation between two genes on a microarray

<p>Abstract</p> <p>Background</p> <p>The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to experimental conditions could be co-expressed and show similar patterns of expression on a microarray. Using any of a variety of clustering methods or gene network analyses we can partition genes of interest into groups, clusters, or modules based on measures of similarity. Typically, Pearson correlation is used to measure distance (or similarity) before implementing a clustering algorithm. Pearson correlation is quite susceptible to outliers, however, an unfortunate characteristic when dealing with microarray data (well known to be typically quite noisy.)</p> <p>Results</p> <p>We propose a resistant similarity metric based on Tukey's biweight estimate of multivariate scale and location. The resistant metric is simply the correlation obtained from a resistant covariance matrix of scale. We give results which demonstrate that our correlation metric is much more resistant than the Pearson correlation while being more efficient than other nonparametric measures of correlation (e.g., Spearman correlation.) Additionally, our method gives a systematic gene flagging procedure which is useful when dealing with large amounts of noisy data.</p> <p>Conclusion</p> <p>When dealing with microarray data, which are known to be quite noisy, robust methods should be used. Specifically, robust distances, including the biweight correlation, should be used in clustering and gene network analysis.</p

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Freshwater Seepage Into Sediments of the Shelf, Shelf Edge, and Continental Slope of the Canadian Beaufort Sea

Long‐term warming of the continental shelf of the Canadian Beaufort Sea caused by the transgression associated with the last deglaciation may be causing decomposition of relict offshore subsea permafrost and gas hydrates. To evaluate this possibility, pore waters from 118 sediment cores up to 7.3‐m long were taken on the shelf and slope and analyzed for chloride concentrations and δ180 and δD composition. We observed downcore decreases in pore waters Cl− concentration in sediments from all sites from the inner shelf (<20‐m water depth), from the shelf edge, from the outer slope (down to 1,000‐m water depths), and from localized shelf features such as midshelf pingo‐like features and inner shelf pockmarks. In contrast, pore water freshening is absent from all investigated cores of the Mackenzie Trough. Downcore pore waters Cl− concentration decreases indicate regional widespread freshwater seepage. Extrapolations to zero Cl− of pore water Cl− versus δ180 regression lines indicate that freshwaters in these environments carry different isotope signatures and thus are sourced from different reservoirs. These isotopic signatures indicate that freshening of shelf sediments pore waters is a result of downward infiltration of Mackenzie River water, freshening of shelf edge sediments is due to relict submarine permafrost degradation or gas hydrate decomposition under the shelf, and freshening of slope sediments is consistent with regional groundwater flow and submarine groundwater discharge as far as 150 km from shore. These results confirm ongoing decomposition of offshore permafrost and suggest extensive current groundwater discharge far from the coast

Analyse temporelle et structurale de la relation orthoptères-végétation

The authors carry out a study on a grasshopper community in a protected zone of the Limousin region. The relationship between the floristic composition of the stations and the grasshopper composition is evaluated over three months (July, August and September) with NMDS analysis and Mantel's test. Correlations (Spearman rho) between vegetation factors (height, diversity, compacity and relative humidity) and the density of Orthoptera are also studied. Orthopteran community is more closely adjusted to floristic composition in August and September than in July. Density and diversity of Orthoptera are linked to vegetation compacity and diversity, and specially to the group Gramineae, Cyperaceae and Joncaceae. Results are commented according to the literature