Quantification of transcription factor expression from Arabidopsis images.


Journal Article

MOTIVATION: Confocal microscopy has long provided qualitative information for a variety of applications in molecular biology. Recent advances have led to extensive image datasets, which can now serve as new data sources to obtain quantitative gene expression information. In contrast to microarrays, which usually provide data for many genes at one time point, these image data provide us with expression information for only one gene, but with the advantage of high spatial and/or temporal resolution, which is often lostin microarray samples. RESULTS: We have developed a prototype for the automatic analysis of Arabidopsis confocal images, which show the expression of a single transcription factor by means of GFP reporter constructs. Using techniques from image registration, we are able to address inherent problems of non-rigid transformation and partial mapping, and obtain relative expression values for 13 different tissues in Arabidopsis roots. This provides quantitative information with high spatial resolution, which accurately represents the underlying expression values within the organism. We validate our approach on a data set of 122 images depicting expression patterns of 30 transcription factors, both in terms of registration accuracy, as well as correlation with cell-sorted microarray data. Approaches like this will be useful to lay the groundwork to reconstruct regulatory networks on the level of tissues or even individual cells. AVAILABILITY: Upon request from the authors.

Full Text

Duke Authors

Cited Authors

  • Mace, DL; Lee, J-Y; Twigg, RW; Colinas, J; Benfey, PN; Ohler, U

Published Date

  • July 15, 2006

Published In

Volume / Issue

  • 22 / 14

Start / End Page

  • e323 - e331

PubMed ID

  • 16873489

Pubmed Central ID

  • 16873489

Electronic International Standard Serial Number (EISSN)

  • 1367-4811

Digital Object Identifier (DOI)

  • 10.1093/bioinformatics/btl228


  • eng

Conference Location

  • England