AIM To investigate the gene expression profiles of acute promyelocytic leukemia (APL) cell line NB4 treated with arsenic trioxide (As2O3) using cDNA microarray. METHODS Two cDNA probes were prepared through reverse transcription from mRNA of NB4 cells treated with or without arsenic trioxide. The probes were labeled with Cy3 and Cy5 fluorescence dyes individually, hybridized with cDNA microar...

The strategy used to create and annotate a 7872 cDNA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6300 unique genes, as determined by BLASTN and TBLASTX similarity search against the human and mouse UniGene and draft human genome sequence databases (build 34). Sequences on the array were annotated with gene ontology (GO) terms, t...

The objective of this work was to investigate the segmentation ability of the Fuzzy Gaussian Mixture Models (FGMM) clustering algorithm, applied on complementary DNA (cDNA) images. A Simulated Microarray image of 200 cells, each containing one spot, was produced following standard established procedure. An automatic gridding process was developed and applied on the microarray image for the task...

MOTIVATION Background correction is an important preprocess in cDNA microarray data analysis. A variety of methods have been used for this purpose. However, many kinds of backgrounds, especially inhomogeneous ones, cannot be estimated correctly using any of the existing methods. In this paper, we propose the use of the TV+L1 model, which minimizes the total variation (TV) of the image subject t...

BACKGROUND Advances in molecular and computational biology have led to the development of powerful, high-throughput methods for analysis of differential gene expression, which are opening up new opportunities in genomic medicine. DNA microarray technology has been enthusiastically integrated into basic biomedical research and will eventually become a molecular monitoring tool for various clinic...

We compared the gene expression among four clinical and five environmental V. vulnificus isolates, using a cDNA microarray containing 131 genes possibly associated with pathogenicity, transport, signal transduction, and gene regulations in the pathogen. cDNAs from total RNAs of these isolates were hybridized into the cDNA microarray using the cDNA of the wild-type strain MO6/24-O as a reference...

Currently there are over 1,000,000 human expressed sequence tag (EST) sequences available on the public database, representing perhaps 50-90% of all human genes. The cDNA microarray technique is a recently developed tool that exploits this wealth of information for the analysis of gene expression. In this method, DNA probes representing cDNA clones are arrayed onto a glass slide and interrogate...

The oligo microarray (DNA chip) technology in recent years has a significant impact on genomic study. Many fields such as gene discovery, drug discovery, toxicological research and disease diagnosis, will certainly benefit from its use. A microarray is an orderly arrangement of thousands of DNA fragments where each DNA fragment is a probe (or a fingerprint) of a gene/cDNA. It is important that ...

We show here that the amount of labeled cDNA and its specific activity can play a significant role in the quantitation of microarray experiments. Standard reverse transcription of 2 microg total bacterial RNA with concomitant incorporation of cyanine dye-conjugated nucleotides did not produce enough label for optimal hybridization results in our Mycobacterium tuberculosis DNA microarray. Theref...