Methods for evaluating gene expression from Affymetrix microarray datasets

<p>Abstract</p> <p>Background</p> <p>Affymetrix high density oligonucleotide expression arrays are widely used across all fields of biological research for measuring genome-wide gene expression. An important step in processing oligonucleotide microarray data is to produce a single value for the gene expression level of an RNA transcript using one of a growing number of statistical methods. The challenge for the researcher is to decide on the most appropriate method to use to address a specific biological question with a given dataset. Although several research efforts have focused on assessing performance of a few methods in evaluating gene expression from RNA hybridization experiments with different datasets, the relative merits of the methods currently available in the literature for evaluating genome-wide gene expression from Affymetrix microarray data collected from real biological experiments remain actively debated.</p> <p>Results</p> <p>The present study reports a comprehensive survey of the performance of all seven commonly used methods in evaluating genome-wide gene expression from a well-designed experiment using Affymetrix microarrays. The experiment profiled eight genetically divergent barley cultivars each with three biological replicates. The dataset so obtained confers a balanced and idealized structure for the present analysis. The methods were evaluated on their sensitivity for detecting differentially expressed genes, reproducibility of expression values across replicates, and consistency in calling differentially expressed genes. The number of genes detected as differentially expressed among methods differed by a factor of two or more at a given false discovery rate (FDR) level. Moreover, we propose the use of genes containing single feature polymorphisms (SFPs) as an empirical test for comparison among methods for the ability to detect true differential gene expression on the basis that SFPs largely correspond to <it>cis</it>-acting expression regulators. The PDNN method demonstrated superiority over all other methods in every comparison, whilst the default Affymetrix MAS5.0 method was clearly inferior.</p> <p>Conclusion</p> <p>A comprehensive assessment of seven commonly used data extraction methods based on an extensive barley Affymetrix gene expression dataset has shown that the PDNN method has superior performance for the detection of differentially expressed genes.</p

Reinterpreting the age of the uppermost ‘Old Red Sandstone’ and Early Carboniferous in Scotland

In Scotland, the base of the Ballagan Formation has traditionally been placed at the first grey mudstone within a contiguous Late Devonian to Carboniferous succession. This convention places the Devonian–Carboniferous boundary within the Old Red Sandstone (ORS) Kinnesswood Formation. The consequences of this placement are that tetrapods from the Ballagan Formation were dated as late Tournaisian in age and that the ranges of typically Devonian fish found in the Kinnesswood Formation continued into the Carboniferous. The Pease Bay specimen of the fish Remigolepis is from the Kinnesswood Formation. Comparisons with its range in Greenland, calibrated against spores, show it was Famennian in age. Detailed palynological sampling at Burnmouth from the base of the Ballagan Formation proves that the early Tournaisian spore zones (VI and HD plus Cl 1) are present. The Schopfites species that occurs through most of the succession is Schopfites delicatus rather than Schopfites claviger. The latter species defines the late Tournaisian CM spore zone. The first spore assemblage that has been found in Upper ‘ORS' strata underlying the Ballagan Formation (Preston, Whiteadder Water), contains Retispora lepidophyta and is from the early latest Famennian LL spore zone. The spore samples are interbedded with volcaniclastic debris, which shows that the Kelso Volcanic Formation is, in part, early latest Famennian in age. These findings demonstrate that the Ballagan Formation includes most of the Tournaisian with the Devonian–Carboniferous boundary positioned close to the top of the Kinnesswood Formation. The Stage 6 calcrete at Pease Bay can be correlated to the equivalent section at Carham, showing that it represents a time gap equivalent to the latest Famennian glaciation(s). Importantly, some of the recently described Ballagan Formation tetrapods are older than previously dated and now fill the key early part of Romer's Gap

The terrestrial landscapes of tetrapod evolution in earliest Carboniferous seasonal wetlands of SE Scotland

The Lower Mississippian (Tournaisian) Ballagan Formation in SE Scotland yields tetrapod fossils that provide fresh insights into the critical period when these animals first moved onto land. The key to understanding the palaeoenvironments where they lived is a detailed analysis of the sedimentary architecture of this formation, one of the thickest and most completely documented examples of a coastal floodplain and marginal marine succession from this important transitional time anywhere in the world. Palaeosols are abundant, providing a unique insight into the early Carboniferous habitats and climate. More than 200 separate palaeosols are described from three sections through the formation. The palaeosols range in thickness from 0.02 to 1.85 m and are diverse: most are Entisols and Inceptisols (63%), indicating relatively brief periods of soil development. Gleyed Inseptisols and Vertisols are less common (37%). Vertisols are the thickest palaeosols (up to 185 cm) in the Ballagan Formation and have common vertic cracks. Roots are abundant through all the palaeosols, from shallow mats and thin hair-like traces to sporadic thicker root traces typical of arborescent lycopods. Geochemical, isotope and clay mineralogical analyses of the palaeosols indicate a range in soil alkalinity and amount of water logging. Estimates of mean annual rainfall from palaeosol compositions are 1000 –1500 mm per year. The high mean annual rainfall and variable soil alkalinities contrast markedly with dry periods that developed deep penetrating cracks and evaporite deposits. It is concluded that during the early Carboniferous, this region experienced a sharply contrasting seasonal climate and that the floodplain hosted a mosaic of closely juxtaposed but distinct habitats in which the tetrapods lived. The diversification of coastal floodplain environments identified here may link to the evolution and movement of tetrapods into the terrestrial realm

Palaeogeography of tropical seasonal coastal wetlands in northern Britain during the early Mississippian Romer's Gap

The lower Mississippian Ballagan Formation of northern Britain is one of only two successions worldwide to yield the earliest known tetrapods with terrestrial capability following the end-Devonian mass extinction event. Studies of the sedimentary environments and habitats in which these beasts lived have been an integral part of a major research project into how, why and under what circumstances this profound step in the evolution of life on Earth occurred. Here, a new palaeogeographic map is constructed from outcrop data integrated with new and archived borehole material. The map shows the extent of a very low-relief coastal wetland developed along the tropical southern continental margin of Laurussia. Coastal floodplains in the Midland Valley and Tweed basins were separated from the marginal marine seaway of the Northumberland–Solway Basin to the south by an archipelago of more elevated areas. A complex mosaic of sedimentary environments was juxtaposed, and included fresh and brackish to saline and hypersaline lakes, a diverse suite of floodplain palaeosols and a persistent fluvial system in the east of the region. The strongly seasonal climate led to the formation of evaporite deposits alternating with flooding events, both meteoric and marine. Storm surges drove marine floods from the SW into both the western Midland Valley and Northumberland–Solway Basin; marine water also flooded into the Tweed Basin and Tayside in the east. The Ballagan Formation is a rare example in the geological record of a tropical, seasonal coastal wetland that contains abundant, small-scale evaporite deposits. The diverse sedimentary environments and palaeosol types indicate a network of different terrestrial and aquatic habitats in which the tetrapods lived

Early Mississippian evaporites of coastal tropical wetlands

Extensive evaporites in Lower Mississippian successions from palaeoequatorial regions are commonly used as evidence for an arid to semi‐arid palaeoclimate. However, in this article, detailed studies of evaporites and their context refute this interpretation. Detailed sedimentological and petrographical analysis of the Lower Mississippian of northern Britain, is combined with archived log data from more than 40 boreholes across southern Scotland, northern England and Northern Ireland, and published literature from Canada. Two key cores from the Tweed Basin and the northern margin of the Northumberland – Solway Basin contain 178 evaporite intervals and reveal twelve distinct forms of gypsum and anhydrite across seven facies that are associated with planar laminated siltstone and intercalated thin beds of ferroan dolostone. Nodular gypsum and anhydrite, typically in intervals <1 to 2 m thick, are integral components of the succession. Nodular evaporite occurs within about 1 m of a palaeosurface, but most evaporite deposits represent ephemeral brine pans to semi‐permanent hypersaline lakes or salinas on a floodplain that was subjected periodically to storm surges introducing marine waters. Formation of evaporites under a strongly seasonal climate in a coastal wetland is supported by palaeosol types and geochemical proxies, and from palaeobotanical evidence published previously. Although 65% of modern equatorial areas experience a strongly seasonal climatic regime, salinas and sabkhas are a minor component today in comparison with the evidence from these Lower Mississippian successions. This implies that the earliest terrestrial environments were complex and dynamic, providing a diverse range of habitats in which the early tetrapods became terrestrialized and represent a setting that is rarely preserved in the geological record

Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data

It is well known that Affymetrix microarrays are widely used to predict genome-wide gene expression and genome-wide genetic polymorphisms from RNA and genomic DNA hybridization experiments, respectively. It has recently been proposed to integrate the two predictions by use of RNA microarray data only. Although the ability to detect single feature polymorphisms (SFPs) from RNA microarray data has many practical implications for genome study in both sequenced and unsequenced species, it raises enormous challenges for statistical modelling and analysis of microarray gene expression data for this objective. Several methods are proposed to predict SFPs from the gene expression profile. However, their performance is highly vulnerable to differential expression of genes. The SFPs thus predicted are eventually a reflection of differentially expressed genes rather than genuine sequence polymorphisms. To address the problem, we developed a novel statistical method to separate the binding affinity between a transcript and its targeting probe and the parameter measuring transcript abundance from perfect-match hybridization values of Affymetrix gene expression data. We implemented a Bayesian approach to detect SFPs and to genotype a segregating population at the detected SFPs. Based on analysis of three Affymetrix microarray datasets, we demonstrated that the present method confers a significantly improved robustness and accuracy in detecting the SFPs that carry genuine sequence polymorphisms when compared to its rivals in the literature. The method developed in this paper will provide experimental genomicists with advanced analytical tools for appropriate and efficient analysis of their microarray experiments and biostatisticians with insightful interpretation of Affymetrix microarray data

Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes

In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis