Quantification of transcription factor expression from Arabidopsis images.
BACKGROUND
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.


BACKGROUND
Upon request from the authors.
Mace
Daniel L
DL
Institute for Genome Science and Policy, Duke University, Durham, NC 27708, USA.
Lee
Ji-Young
JY
Twigg
Richard W
RW
Colinas
Juliette
J
Benfey
Philip N
PN
Ohler
Uwe
U
D029681:Arabidopsis Proteins / Q000032:analysis / Q000378:metabolism*; D002478:Cells, Cultured; D015870:Gene Expression / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D014157:Transcription Factors / Q000032:analysis / Q000378:metabolism*
D029681:Arabidopsis Proteins; D014157:Transcription Factors