Monitoring gene expression and amplification through mid-density oligonucleotide array platforms

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...

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...

Study of Gene Expression Signatures for the Diagnosis of Pediatric Acute Lymphoblastic Leukemia (ALL) Through Gene Expression Array Analyses

Background: Acute lymphoblastic leukemia (ALL) as the most common malignancy in children is associated with high mortality and significant relapse. Currently, the non-invasive diagnosis of pediatric ALL is a main challenge in the early detection of patients. In the present study, a systems biology approach was used through network-based analysis to identify the key candidate genes related to AL...