OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

Background - High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be designed when a reference genome of the species at hand were completely sequenced, when this genome were completely annotated and when the genetic variation of the sampled individuals were completely known. Unfortunately there is not a single species for which such a complete data set is available. Therefore, it is important that probe annotation can be updated frequently for optimal interpretation of microarray experiments. Results - In this paper we present OligoRAP, a pipeline to automatically update the annotation of oligo libraries and estimate oligo target specificity. OligoRAP uses a reference genome assembly with Ensembl and Entrez Gene annotation supplemented with a set of unmapped transcripts derived from RefSeq and UniGene to handle assembly gaps. OligoRAP produces alignments of each oligo with the reference assembly as well as with unmapped transcripts. These alignments are re-mapped to the annotation sources, which results in a concise, as complete as possible and up-to-date annotation of the oligo library. The building blocks of this pipeline are BioMoby web services creating a highly modular and distributed system with a robust, remote programmatic interface. OligoRAP was used to update the annotation for a subset of 791 oligos from the ARK-Genomics 20 K chicken array, which were selected as starting material for the oligo annotation session of the EADGENE/SABRE Post-analysis workshop. Based on the updated annotation about one third of these oligos is problematic with regard to target specificity. In addition, the accession numbers or ids the oligos were originally designed for no longer exist in the updated annotation for almost half of the oligos. Conclusion - As microarrays are designed on incomplete data, it is important to update probe annotation and check target specificity regularly. OligoRAP provides both and due to its design based on BioMoby web services it can easily be embedded as an oligo annotation engine in customised applications for microarray data analysis. The dramatic difference in updated annotation and target specificity for the ARK-Genomics 20 K chicken array as compared to the original data emphasises the need for regular updates

A New Nonlinear Compounding Technique for Ultrasound B-mode Medical Imaging

Compounding techniques have been used in ultra-fast ultrasound imaging to improve image quality by reducing clutter noise, smoothing speckle variance and enhancing its spatial resolution at the cost of reducing frame rate. However, the reduction of clutter noise and side lobes inside the anechoic regions is minimal when combining conventional spatial compounding and delay-and-sum (DAS) beamforming. Despite the availability of advanced beamforming algorithms such as filtered-delay-multiply-and-sum (FDMAS), its prevalence is hindered by relatively high computational cost. In this study, a new nonlinear compounding technique known as filtered multiply and sum (FMAS) was proposed to improve the B-mode image quality without increasing the overall computational complexity. With three compunding angles, the lateral resolution for DAS-FMAS was improved by 36% and 19% compared to DAS and FDMAS. The proposed DAS-FMAS technique also provided improvements of 14.1 dB and 7.29 dB in contrast ratio than DAS and FDMAS

Microarray data mining using Bioconductor packages

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Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

Background - Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. Results - IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines. For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. Conclusion - In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotatio

Regional regulation of transcription in the chicken genome

<p>Abstract</p> <p>Background</p> <p>Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis.</p> <p>Results</p> <p>We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes.</p> <p>Conclusions</p> <p>Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution.</p> <p>The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: <url>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108</url></p

A Novel Two-Dimensional Displacement Estimation for Angled Shear Wave Elastography

This study aimed to estimate angled tissue motion for shear wave compounding applications. Shear wave elastography produces the quantitative elasticity biomarker for assessing the health status of tissues. In sheer wave compounding, steered shear waves are generated with different angles, and individual angle elasticity maps are averaged to improve tissue stiffness reconstruction. When shear waves are steered and the tissue motion is generated in multiple directions, traditional one dimensional (1D) displacement estimation fails in capturing actual shear wave amplitude and direction. This study investigated the use of two dimensional (2D) kernel to track angular shear wave motion, which resulted in the underestimation of displacement values. Consequently, a new method named as 2D proposed (2D-P) was used to calculate both axial and lateral motion components separately using 1D axial and lateral kernels. Final results indicated that, the proposed scheme produced an average improvement of 2.01 μm and 4.4 μm compared with the 1D axial cross correlation and 2D cross correlation based methods, respectively

Classification of fibroglandular tissue distribution in the breast based on radiotherapy planning CT

Accurate segmentation of breast tissues is required for a number of applications such as model based deformable registration in breast radiotherapy. The accuracy of breast tissue segmentation is affected by the spatial distribution (or pattern) of fibroglandular tissue (FT). The goal of this study was to develop and evaluate texture features, determined from planning computed tomography (CT) data, to classify the spatial distribution of FT in the breas

Optimizing the lateral beamforming step for filtered-delay multiply and sum beamforming to improve active contour segmentation using ultrafast ultrasound imaging

As an alternative to delay-and-sum beamforming, a novel beamforming technique called filtered-delay multiply and sum (FDMAS) was introduced recently to improve ultrasound B-mode image quality. Although a considerable amount of work has been performed to evaluate FDMAS performance, no study has yet focused on the beamforming step size, , in the lateral direction. Accordingly, the performance of FDMAS was evaluated in this study by fine-tuning to find its optimal value and improve boundary definition when balloon snake active contour (BSAC) segmentation was applied to a B-mode image in ultrafast imaging. To demonstrate the effect of altering in the lateral direction on FDMAS, measurements were performed on point targets, a tissue-mimicking phantom and in vivo carotid artery, by using the ultrasound array research platform II equipped with one 128-element linear array transducer, which was excited by 2-cycle sinusoidal signals. With 9-angle compounding, results showed that the lateral resolution (LR) of the point target was improved by 67.9% and 81.2%, when measured at −6 dB and −20 dB respectively, when was reduced from to . Meanwhile the image contrast ratio (CR) measured on the CIRS phantom was improved by 10.38 dB at the same reduction and the same number of compounding angles. The enhanced FDMAS results with lower side lobes and less clutter noise in the anechoic regions provides a means to improve boundary definition on a B-mode image when BSAC segmentation is applied

The influence of soil communities on the temperature sensitivity of soil respiration

Soil respiration represents a major carbon flux between terrestrial ecosystems and the atmosphere, and is expected to accelerate under climate warming. Despite its importance in climate change forecasts, however, our understanding of the effects of temperature on soil respiration (RS) is incomplete. Using a metabolic ecology approach we link soil biota metabolism, community composition and heterotrophic activity, to predict RS rates across five biomes. We find that accounting for the ecological mechanisms underpinning decomposition processes predicts climatological RS variations observed in an independent dataset (n = 312). The importance of community composition is evident because without it RS is substantially underestimated. With increasing temperature, we predict a latitudinal increase in RS temperature sensitivity, with Q10 values ranging between 2.33 ±0.01 in tropical forests to 2.72 ±0.03 in tundra. This global trend has been widely observed, but has not previously been linked to soil communities

The lncRNA HOTAIR transcription is controlled by HNF4α-induced chromatin topology modulation

The expression of the long noncoding RNA HOTAIR (HOX Transcript Antisense Intergenic RNA) is largely deregulated in epithelial cancers and positively correlates with poor prognosis and progression of hepatocellular carcinoma and gastrointestinal cancers. Furthermore, functional studies revealed a pivotal role for HOTAIR in the epithelial-to-mesenchymal transition, as this RNA is causal for the repressive activity of the master factor SNAIL on epithelial genes. Despite the proven oncogenic role of HOTAIR, its transcriptional regulation is still poorly understood. Here hepatocyte nuclear factor 4-α (HNF4α), as inducer of epithelial differentiation, was demonstrated to directly repress HOTAIR transcription in the mesenchymal-to epithelial transition. Mechanistically, HNF4α was found to cause the release of a chromatin loop on HOTAIR regulatory elements thus exerting an enhancer-blocking activity