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Bioinformatics Advance Access originally published online on July 16, 2009
Bioinformatics 2009 25(19):2581-2587; doi:10.1093/bioinformatics/btp437
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Reconstructing spatiotemporal gene expression data from partial observations

Dustin A. Cartwright 1,*, Siobhan M. Brady 2,3,4,5,{dagger}, David A. Orlando 2,3,6,{dagger}, Bernd Sturmfels 1 and Philip N. Benfey 2,3

1Department of Mathematics, University of California, Berkeley, CA 94704, 2Department of Biology, 3Duke Center for Systems Biology, Duke University, Durham, NC 27708, 4Department of Plant Biology, 5Genome Center, University of California, Davis, CA 95616 and 6Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Developmental transcriptional networks in plants and animals operate in both space and time. To understand these transcriptional networks it is essential to obtain whole-genome expression data at high spatiotemporal resolution. Substantial amounts of spatial and temporal microarray expression data previously have been obtained for the Arabidopsis root; however, these two dimensions of data have not been integrated thoroughly. Complicating this integration is the fact that these data are heterogeneous and incomplete, with observed expression levels representing complex spatial or temporal mixtures.

Results: Given these partial observations, we present a novel method for reconstructing integrated high-resolution spatiotemporal data. Our method is based on a new iterative algorithm for finding approximate roots to systems of bilinear equations.

Availability: Source code for solving bilinear equations is available at http://math.berkeley.edu/~dustin/bilinear/. Visualizations of reconstructed patterns on a schematic Arabidopsis root are available at http://www.arexdb.org/.

Contact: dustin{at}math.berkeley.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Olga Troyanskaya

{dagger} The authors wish it to be known that, in their opinion, the second and third authors should be regarded as joint Second authors.

Received on April 27, 2009; revised on July 2, 2009; accepted on July 13, 2009

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