title: Extracting information from cDNA arrays.
abstract: High-density DNA arrays allow measurements of gene expression levels (messenger RNA abundance) for thousands of genes simultaneously. We analyze arrays with spotted cDNA used in monitoring of expression profiles. A dilution series of a mouse liver probe is deployed to quantify the reproducibility of expression measurements. Saturation effects limit the accessible signal range at high intensities. Additive noise and outshining from neighboring spots dominate at low intensities. For repeated measurements on the same filter and filter-to-filter comparisons correlation coefficients of 0.98 are found. Next we consider the clustering of gene expression time series from stimulated human fibroblasts which aims at finding co-regulated genes. We analyze how preprocessing, the distance measure, and the clustering algorithm affect the resulting clusters. Finally we discuss algorithms for the identification of transcription factor binding sites from clusters of co-regulated genes. (c) 2001 American Institute of Physics.
authors.affiliation: Institute for Theoretical Biology, Humboldt-University, Invalidenstr. 43, D-10115 Berlin, Germany.
authors.forename: Hanspeter
authors.initials: H
authors.lastname: Herzel
authors.forename: Dieter
authors.initials: D
authors.lastname: Beule
authors.forename: Szymon
authors.initials: S
authors.lastname: Kielbasa
authors.forename: Jan
authors.initials: J
authors.lastname: Korbel
authors.forename: Christine
authors.initials: C
authors.lastname: Sers
authors.forename: Arif
authors.initials: A
authors.lastname: Malik
authors.forename: Holger
authors.initials: H
authors.lastname: Eickhoff
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Johannes
authors.initials: J
authors.lastname: Schuchhardt