Gene expression analysis following hypoxia–reoxygenation in rat gastric epithelial cells using a high-density oligonucleotide array

From features to expression: High-density oligonucleotide array analysis revisited

One of the most popular tools for large scale gene expression studies are highdensity oligonucleotide (GeneChip R ) arrays. These currently have 16-20 small probes (“features”) for evaluating the transcript abundance of each gene. In addition, each probe is accompanied by a mismatched probe (MM) designed as a control for non-specificity. An algorithm is presented to compute comparative expressi...

From features to expression: High-density oligonucleotide array analysis revisited.

Osmolarity Regulates Gene Expression in Intervertebral Disc Cells Quantifiedwith High Density Oligonucleotide Array Technology

INTRODUCTION: Cells of the intervertebral disc respond to mechanical and biophysical stimuli in their environment, including deformations, hydrostatic and osmotic pressures [1]. Previous studies have shown that fibrochondrocytes of the disc respond to altered osmotic pressure with changes in post-translational biosynthesis of proteoglycans (i.e., S-incorporation) [2, 3], as well as changes in g...

Algorithms for high-density oligonucleotide array.

As a global gene expression-monitoring tool, high-density oligonucleotide arrays (HDAs), accelerate biological and drug discovery processes. Computational considerations affect several key issues, from array design and accurate gene expression level determination to various aspects of the biological analysis of cell functions and gene networks. This review highlights recent progress in ideas an...

Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data.

Algorithms for performing feature extraction and normalization on high-density oligonucleotide gene expression arrays, have not been fully explored, and the impact these algorithms have on the downstream analysis is not well understood. Advances in such low-level analysis methods are essential to increase the sensitivity and specificity of detecting whether genes are present and/or differential...