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Within the fold: assessing differential expression measures and reproducibility in microarray assays.
- Source :
-
Genome biology [Genome Biol] 2002 Oct 24; Vol. 3 (11), pp. research0062. Date of Electronic Publication: 2002 Oct 24. - Publication Year :
- 2002
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Abstract
- Background: 'Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed between query and reference samples. More accurate measures of differential expression and effective data-normalization strategies are required to identify high-confidence sets of genes with biologically meaningful changes in transcription. Further, the analysis of a large number of expression profiles is facilitated by a common reference sample, the construction of which must be carefully addressed.<br />Results: We carried out a series of 'self-self' hybridizations in which aliquots of the same RNA sample were labeled separately with Cy3 and Cy5 fluorescent dyes and co-hybridized to the same microarray. From this, we can analyze the intensity-dependent behavior of microarray data, define a statistically significant measure of differential expression that exploits the structure of the fluorescent signals, and measure the inherent reproducibility of the technique. We also devised a simple procedure for identifying and eliminating low-quality data for replicates within and between slides. We examine the properties required of a universal reference RNA sample and show how pooling a small number of samples with a diverse representation of expressed genes can outperform more complex mixtures as a reference sample.<br />Conclusion: Analysis of cell-line samples can identify systematic structure in measured gene-expression levels. A general procedure for analyzing cDNA microarray data is proposed and validated. We show that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines.
- Subjects :
- Brain Neoplasms genetics
Carcinoma genetics
Colonic Neoplasms genetics
DNA, Complementary analysis
Female
Gene Expression Regulation, Neoplastic genetics
Humans
Male
Nucleic Acid Hybridization methods
Organ Specificity genetics
Ovarian Neoplasms genetics
Pancreatic Neoplasms genetics
RNA, Neoplasm analysis
Reference Values
Testicular Neoplasms genetics
Tumor Cells, Cultured
Gene Expression Profiling methods
Oligonucleotide Array Sequence Analysis methods
Subjects
Details
- Language :
- English
- ISSN :
- 1474-760X
- Volume :
- 3
- Issue :
- 11
- Database :
- MEDLINE
- Journal :
- Genome biology
- Publication Type :
- Academic Journal
- Accession number :
- 12429061
- Full Text :
- https://doi.org/10.1186/gb-2002-3-11-research0062