A novel microarray gene selection method based on consistency

Consistency modeling for gene selection is a new topic emerging from recent cancer bioinformatics research. The result of classification or clustering on a training set was often found very different from the same operations on a testing set. Here, we address this issue as a consistency problem. We propose a new concept of performance-based consistency and a new novel gene selection method, Genetic Algorithm Gene Selection method in terms of consistency (GAGSc). The proposed consistency concept and GAGSc method were investigated on eight benchmark microarray and proteomic datasets. The experimental results show that the different microarray datasets have different consistency characteristics, and that better consistency can lead to an unbiased and reproducible outcome with good disease prediction accuracy. More importantly, GAGSc has demonstrated that gene selection, with the proposed consistency measurement, is able to enhance the reproducibility in microarray diagnosis experiments

Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

<p>Abstract</p> <p>Background</p> <p>Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation.</p> <p>Results</p> <p>We have developed a method called Base Skew Double Triangle (BSDT) for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture), except for some microchromosomes. No other organisms studied (18 species) show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens.</p> <p>Conclusion</p> <p>Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic, present not only in chickens, but also remained or developed in some mammals during evolution. Special aspects of bird metabolism related to e.g. flight may be the reason why birds evolved or retained the skew correlation. Our analysis also indicated that repetitive DNA sequence elements need to be taken into account in studying the evolution of the correlation between AT and CG skews.</p

Untranslated parts of genes interpreted: making heads or tails of high-throughput transcriptomic data via computational methods

The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by where transcription starts and ends on a genomic locus. The extent of alternative transcription start and alternative poly-adenylation has been revealed by sequencing methods focused on the ends of transcripts, but the application of these methods is not yet widely adopted by the community. In this review we highlight the importance of defining the untranslated parts of transcripts and suggest that computational methods applied to standard high-throughput technologies are a useful alternative to the expertise-demanding 5’ and 3’ sequencing. We present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events, focusing on technical challenges and arguing for the need to include better normalization of the data and more appropriate statistical models of the expected variation in the signal

Locomotory manoeuvres of beetles responding to non-directional humidity clues

Imperial Users onl

Non-chemical control methods against cabbage root flies delia radicum and delia floralis (anthomyiidae)

vokkirjasto Aj-KKaalikärpästen luonnonmukaiset torjuntamenetelmä