A Bioinformatics Approach for Identifying Candidate Transcriptional Regulators of Mesenchyme-to-Epithelium Transitions in Mouse Embryos

J. B. L. Bard, M. S. Lam, James Aitken

Research output: Contribution to journalArticlepeer-review

Abstract

This article reports a method for identifying groups of genes associated with tissues undergoing a particular process during mouse development. Given the Theiler stage at which each tissue starts the process, Boolean intersection analysis identifies genes expressed in some or all of these tissues both before the process starts and once it has started. This analysis is implemented in GXD-search; this tool downloads appropriate gene sets from GXD, the mouse gene expression database, and performs the calculations. Applied to mesenchyme-to-epithelium transitions (MET), GXD-search has identified Crabp1 and six transcriptional regulators (Cited1, Cited2, Meox1, Lhx1, Foxc1, and Foxc2) that are usually expressed in tissues about to undergo this process. Expression pattern analysis of these transcriptional regulators, mutations in each of which affect epithelial development, shows that this gene set is expressed in no other tissues and they are, thus, candidates for regulating MET. GXD-search is downloadable from http://www.aiai.ed.ac.uk/project/biosphere/GXD-search.html. Developmental Dynamics 237:2748-2754, 2008. (C) 2008 Wiley-Liss, Inc.
Original languageEnglish
Pages (from-to)2748-2754
Number of pages7
JournalDevelopmental Dynamics
Volume237
Issue number10
DOIs
Publication statusPublished - Oct 2008

Keywords

  • Boolean analysis
  • data mining
  • gene expression database
  • gene ontology
  • mesenchyme-to-epithelium transition
  • mouse development
  • process genes
  • systems biology

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