Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.

cDNA Microarray Data Normalization

Identification of specific gene expression after exposure to low dose ionizing radiation revealed through integrative analysis of cDNA microarray data and the interactome

Background: Accumulating reports suggest that the biological effects of low- and high- dose ionizing radiation (LDIR and HDIR) are qualitatively different and might cause different effects in human skin. Materials and Methods: To better understand the potential risks of LDIR, we analyzed three cDNA microarray datasets from the Gene Expression Omnibus database. Results: A pathway analysis showed...

Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments

Motivation: Microarray gene expression data is collected at an increasing pace and numerous methods and tools exist for analyzing this kind of data. The aim of this study is to evaluate the effect of the basic statistical processing steps of microarray data on the final outcome for gene expression analysis; these effects are most problematic for one-channel cDNA measurements, but also affect ot...

پاسخ متفاوت سلولهای قلبی به اسیدهای چرب اشباع و غیر اشباع

Introduction & Objective: The link between dietary fat and coronary heart disease has attracted much attention since the effect of long?chain fatty acids (LCFA) on gene transcription has been established, which in part, these effects can be explained by the regulation of gene transcription. In this study, the P19CL6 cardiac cell?line was targeted for the investigation of (i) the effects of long...

Normalization of single-channel DNA array data by principal component analysis

MOTIVATION Detailed comparison and analysis of the output of DNA gene expression arrays from multiple samples require global normalization of the measured individual gene intensities from the different hybridizations. This is needed for accounting for variations in array preparation and sample hybridization conditions. RESULTS Here, we present a simple, robust and accurate procedure for the g...