Extracting information from cDNA arrays

High-density DNA arrays allow measurements of gene expression levels (messe nger RNA abundance) for thousands of genes simultaneously. We analyze array s with spotted cDNA used in monitoring of expression profiles. A dilution s eries of a mouse liver probe is deployed to quantify the reproducibility of expression measurements. Saturation effects limit the accessible signal ra nge at high intensities. Additive noise and outshining from neighboring spo ts dominate at low intensities. For repeated measurements on the same filte r and filter-to-filter comparisons correlation coefficients of 0.98 are fou nd. Next we consider the clustering of gene expression time series from sti mulated human fibroblasts which aims at finding co-regulated genes. We anal yze how preprocessing, the distance measure, and the clustering algorithm a ffect the resulting clusters. Finally we discuss algorithms for the identif ication of transcription factor binding sites from clusters of co-regulated genes. (C) 2001 American Institute of Physics.