Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment.

Journal Article (Review;Journal Article)

A series of large-scale Arabidopsis thaliana microarray expression experiments profiling genome-wide expression across different developmental stages, cell types, and environmental conditions have resulted in tremendous amounts of gene expression data. This gene expression is the output of complex transcriptional regulatory networks and provides a starting point for identifying the dominant transcriptional regulatory modules acting within the plant. Highly co-expressed groups of genes are likely to be regulated by similar transcription factors. Therefore, finding these co-expressed groups can reduce the dimensionality of complex expression data into a set of dominant transcriptional regulatory modules. Determining the biological significance of these patterns is an informatics challenge and has required the development of new methods. Using these new methods we can begin to understand the biological information contained within large-scale expression data sets.

Full Text

Duke Authors

Cited Authors

  • Orlando, DA; Brady, SM; Koch, JD; Dinneny, JR; Benfey, PN

Published Date

  • January 2009

Published In

Volume / Issue

  • 553 /

Start / End Page

  • 57 - 77

PubMed ID

  • 19588101

Pubmed Central ID

  • PMC4164220

Electronic International Standard Serial Number (EISSN)

  • 1940-6029

International Standard Serial Number (ISSN)

  • 1064-3745

Digital Object Identifier (DOI)

  • 10.1007/978-1-60327-563-7_4


  • eng