FlyGEM, a full transcriptome array platform for the Drosophila community

We have constructed a DNA microarray to monitor expression of predicted genes in Drosophila. By using homotypic hybridizations, we show that the array performs reproducibly, that dye effects are minimal, and that array results agree with systematic northern blotting. The array gene list has been extensively annotated and linked-out to other databases. Incyte and the NIH have made the platform available to the community via academic microarray facilities selected by an NIH committee.     

A between-class overlapping filter-based method for transcriptome data analysis

Feature selection algorithms play a crucial role in identifying and discovering important genes for cancer classification. Feature selection algorithms can be broadly categorized into two main groups: filter-based methods and wrapper-based methods. Filter-based methods have been quite popular in the literature due to their many advantages, including computational efficiency, simplistic architecture, and an intuitively simple means of discovering biological and clinical aspects. However, these methods have limitations, and the classification accuracy of the selected genes is less accurate. In this paper, we propose a set of univariate filter-based methods using a between-class overlapping criterion. The proposed techniques have been compared with many other univariate filter-based methods using an acute leukemia dataset. The following properties have been examined: classification accuracy of the selected individual genes and the gene subsets; redundancy check among selected genes using ridge regression and LASSO methods; similarity and sensitivity analyses; functional analysis; and, stability analysis. A comprehensive experiment shows promising results for our proposed techniques. The univariate filter based methods using between-class overlapping criterion are accurate and robust, have biological significance, and are computationally efficient and easy to implement. Therefore, they are well suited for biological and clinical discoveries.     

Bioinformatics as a critical prerequisite to transcriptome and proteome studies

Large-scale genomic studies rely strongly on annotations available in databases to design experimental supports such as arrays or to explain results in term of biological meaning. Most of this information originates from bioinformatic predictions. Their accuracy as well as their relevance to existing biological data are critical in avoiding the misinterpretation of experimental results.     

A liquid crystal pixel array for signal discrimination in array biosensors

A new optical design uses a liquid crystal pixel array (LCPA) to discriminate multiple fluorescence signals on a two-dimensional biosensor array. The LCPA can selectively control the transmission of fluorescence generated from multiple biosensing elements on a planar waveguide. This device sequentially acquires the fluorescence data from the substrate by making multiple individual measurements of the sensing elements on the waveguide. The biosensing elements are patterned according to the pixel layout of the LCPA and optically aligned so that each electronically driven pixel can either transmit or filter out the fluorescence signal as specified by the user. The primary advantage of this system is that a single detection channel (i.e. photomultiplier tube (PMT)) can be used to measure multiple fluorescence signals from a two-dimensional substrate while the LCPA provides for spatial resolution. We evaluate the performance of the LCPA by testing the optical homogeneity of the liquid crystal pixels and linear dynamic range for transmitting light. The LCPA is also used with well-developed biosensing chemistry modified for this optical format.     

Microplate array diagonal gel electrophoresis for cohort studies of microsatellite loci

After PCR amplification, we have achieved precise sizing of trinucleotide and tetranucleotide microsatellite alleles on 96-well open-faced polyacrylamide microplate array diagonal gel electrophoresis (MADGE) gels: two tetranucleotide repeats, HUMTHOI (five alleles 248-263 bp) and DYS390 (eight alleles 200-228 bp), and DYS392, a trinucleotide repeat (eight alleles 210-231 bp). A gel matrix of Duracryl, a high mechanical strength polyacrylamide derivative, and appropriate ionic conditions provide the 1.3%-1.5% band resolution required. No end-labeling of primers is needed, as the sensitive Vistra Green intercalating dye is used for the visualization of bands. Co-run markers bracketing the PCR fragments ensure accurate sizing without inter-lane variability. Electrophoresis of multiple gels in a thermostatically controlled tank allows up to 1000 samples to be run in 90 min. Gel images were analyzed using a Fluorlmager 595 fluorescent scanning system, and alleles were identified using Phoretix software for band migration measurement and Microsoft Excel to compute fragment sizes. Estimated sizes were interpolated precisely to achieve accurate binning. Microsatellite-MADGE represents a utilitarian methodfor high-throughput genotyping in cohort studies, using standard laboratory equipment.     

Analysis of array CGH data for cancer studies using fused quantile regression

MOTIVATION: The identification of DNA copy number changes provides insights that may advance our understanding of initiation and progression of cancer. Array-based comparative genomic hybridization (array-CGH) has emerged as a technique allowing high-throughput genome-wide scanning for chromosomal aberrations. A number of statistical methods have been proposed for the analysis of array-CGH data. In this article, we consider a fused quantile regression model based on three motivations: (1) quantile regression may provide a more comprehensive picture for the ratio profile of copy numbers than the standard mean regression approach; (2) for simplicity, most available methods assume uniform spacing between neighboring clones, while incorporating the information of physical locations of clones may be helpful and (3) most current methods have a set of tuning parameters that must be carefully tuned, which introduces complexity to the implementation. RESULTS: We formulate the detection of regions of gains and losses in a fused regularized quantile regression framework, incorporating physical locations of clones. We derive an efficient algorithm that computes the entire solution path for the resulting optimization problem, and we propose a simple estimate for the complexity of the fitted model, which leads to convenient selection of the tuning parameter. Three published array-CGH datasets are used to demonstrate our approach. AVAILABILITY: R code are available at http://www.stat.lsa.umich.edu/~jizhu/code/cgh/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

A neutral model of transcriptome evolution

Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.     

A substrate combinatorial array for caspases.

An efficient strategy for the synthesis of a tetrapeptidyl substrate combinatorial array directed toward the caspases is described. Testing of this array with caspases 1 and 4 gave substrate hydrolytic profiles characteristic of each caspase, and permitted the identification of efficiently processed substrates. A comparison of this approach to that using a positional scanning library is presented.