Summary: arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica merging, quality diagnostics and data export. The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured and preprocessed microarray data to high...

SUMMARY Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionall...

We compared the accuracy of microarray measurements obtained with oligonucleotide arrays (GeneChip, Affymetrix) with a laboratory-developed cDNA array by assaying test RNA samples from an experiment using a paradigm known to regulate many genes measured on both arrays. We selected 47 genes represented on both arrays, including both known regulated and unregulated transcripts, and established re...

A two-sample microarray design aims at identifying genes expressed differentially in two-sample cDNA arrays. A two-sample experiment is a commonly used design to compare relative mRNA abundance between two different samples. Several statistical techniques are available for such designs. For the identification of differentially expressed genes, four methods were compared: a fold test, a t-test [...

Our group has been making effort to collect mouse full-length cDNA clones as large scale Mouse cDNA project. It is aiming at collecting all kind of expressed full-length Mouse cDNA clones. The first phase of the project is to make cataloged non-redundant cDNA clone bank. It is necessary for analysis of sequence data and further applications of cDNA clones. We sequence 3’-end part of all cDNA cl...

MOTIVATION Microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. In time-course experiments in which gene expression is monitored over time, we are interested in testing gene expression profiles for different experimental groups. However, no sophisticated analytic methods have yet been proposed to handle time-course experiment data. RESULTS We...

PURPOSE To construct a custom cDNA microarray for comprehensive human retinal gene expression profiling and apply it to the identification of genes that are preferentially expressed in the retina. METHODS A cDNA microarray was constructed based on the predicted human retina gene expression profile according to expressed sequence tag (EST) databases. Gene expression profiles were obtained from...

cDNA microarray analysis was used to examine gene expression profiles in normal female Sprague-Dawley rat mammary gland and in carcinomas induced by the cooked meat-derived carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) and the potent experimental carcinogen 7,12-dimethylbenz[a]anthracene (DMBA). Nine tubulopapillary carcinomas (five from PhIP-treated rats and four from DMBA-...

BACKGROUND The use of DNA microarray technology to study global Schistosoma gene expression has led to the rapid identification of novel biological processes, pathways or associations. Implementation of standardized DNA microarray protocols across laboratories would assist maximal interpretation of generated datasets and extend productive application of this technology. METHODOLOGY/PRINCIPAL ...

MIGS-GPU is a software package for gridding and segmenting cDNA microarray images. MIGS-GPU addresses two stages of microarray image analysis: Firstly, it implements a genetic algorithm in order to efficiently perform the gridding even in poor quality microarray images. Then, it implements a grow-cut algorithm in order to segment the microarray images. Computations for both the gridding and seg...