Effects of sample size on robustness and prediction accuracy of a prognostic gene signature

Background  

Few overlap between independently developed gene signatures and poor inter-study applicability of gene signatures are two of major concerns raised in the development of microarray-based prognostic gene signatures. One recent study suggested that thousands of samples are needed to generate a robust prognostic gene signature.     

Tetracycline-controlled transgene activation using the ROSA26-iM2-GFP knock-in mouse strain permits GFP monitoring of DOX-regulated transgene-expression

Background  

Conditional gene activation is an efficient strategy for studying gene function in genetically modified animals. Among the presently available gene switches, the tetracycline-regulated system has attracted considerable interest because of its unique potential for reversible and adjustable gene regulation.     

Structure and evolution of <Emphasis Type="Italic">Apetala3</Emphasis>, a sex-linked gene in <Emphasis Type="Italic">Silene latifolia</Emphasis>

Background  

The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene AP3 was characterized in the dioecious plant species Silene latifolia. It was suggested that this gene had been transferred from an autosome to the Y chromosome.     

Rooted triple consensus and anomalous gene trees

Background  

Anomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs.     

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm <Emphasis Type="Italic">Silene latifolia</Emphasis>

Background  

Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms.     

Kernel-based distance metric learning for microarray data classification

Background  

The most fundamental task using gene expression data in clinical oncology is to classify tissue samples according to their gene expression levels. Compared with traditional pattern classifications, gene expression-based data classification is typically characterized by high dimensionality and small sample size, which make the task quite challenging.     

Feature extraction and signal processing for nylon DNA microarrays

Background  

High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels.     

A method of precise mRNA/DNA homology-based gene structure prediction

Background  

Accurate and automatic gene finding and structural prediction is a common problem in bioinformatics, and applications need to be capable of handling non-canonical splice sites, micro-exons and partial gene structure predictions that span across several genomic clones.     

Gene knockdown by RNAi in the pea aphid <Emphasis Type="Italic">Acyrthosiphon pisum</Emphasis>

Background  

RNA interference (RNAi) is a powerful method to inhibit gene expression in a sequence specific manner.     

Gene finding in novel genomes

Background  

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.     

On the need for widespread horizontal gene transfers under genome size constraint

Background  

While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery.     

Impact of RNA structure on the prediction of donor and acceptor splice sites

Background  

gene identification in genomic DNA sequences by computational methods has become an important task in bioinformatics and computational gene prediction tools are now essential components of every genome sequencing project. Prediction of splice sites is a key step of all gene structural prediction algorithms.     

Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function

Background  

The purpose of this study is to determine whether or not there exists nonrandom grouping of cis-regulatory elements within gene promoters that can be perceived independent of gene expression data and whether or not there is any correlation between this grouping and the biological function of the gene.     

An interactive tool for visualization of relationships between gene expression profiles

Background  

Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques.     

Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

Background  

When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.