A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays.
BACKGROUND
The radioactivity labeled DNA array platform is a robust and accurate way for a high-throughput measurement of gene expression levels in biological samples. Despite its high degree of sensitivity and reproducibility, this platform has several sources of variation. These are related to the presence of saturation effects in the array images and impede the degree of accuracy at which gene expression levels are determined.


RESULTS
Here we describe a simple, but effective, approach for combining expression data from a series of autoradiographic exposures of variable length. This technique increases the sensitivity of this array platform by detecting low-expressed genes at longer exposures. It also improves the measurement accuracy of highly abundant genes by considering only values from the linear portion of dependency between the exposure times and gene intensities. As a result, the described approach improves the outcome of the subsequent steps of array data normalization and mining.
Querec
Troy D
TD
Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA.
Stoyanova
Radka
R
Ross
Eric
E
Patriotis
Christos
C
D000465:Algorithms; D016477:Artifacts; D001345:Autoradiography / Q000379:methods*; D014408:Biomarkers, Tumor / Q000378:metabolism; D002460:Cell Line; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010051:Ovarian Neoplasms / Q000175:diagnosis / Q000378:metabolism*; D011865:Radioisotope Dilution Technique; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins