title: Quality indicators increase the reliability of microarray data.
abstract: Large-scale gene expression profiling with DNA microarrays opens new dimensions to molecular biology but still lacks the overall precision of traditional low-scale techniques. We developed a novel strategy of data processing linking search stringency to quality indicators for efficient detection of low-level, regulated genes. Using retinoid-induced differentiation of NB-4 promyelocytic cells, the variation of expression profiles between biological duplicates was studied and compared with the changes induced by all-trans retinoic acid (atRA) treatment. An analysis of 4320 genes showed that retinoic acid has mainly geneactivating function in NB-4 cells. Treatment with atRA for 18 hours induced metabolic genes that may be associated with cell differentiation and signaling factors triggering later events leading to apoptosis; cytokine genes were among the highest stimulated by atRA. Notably, we identified a regulatory loop inhibiting MYC action: as MYC was downregulated, a cognate repressor of MYC was upregulated.
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, B.P. 10142, C. U. de Strasbourg, France.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Raffelsberger
authors.forename: Doulaye
authors.initials: D
authors.lastname: Dembélé
authors.forename: Mike G
authors.initials: MG
authors.lastname: Neubauer
authors.forename: Marco M
authors.initials: MM
authors.lastname: Gottardis
authors.forename: Hinrich
authors.initials: H
authors.lastname: Gronemeyer
mesh_terms: D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D019984:Quality Indicators, Health Care; D012044:Regression Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction