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Bioinformatics Techniques for Understanding and Analyzing Tree Gene Expression Data

  • Lewis LukensEmail author
  • Gregory Downs
Chapter

Abstract

There is great interest in enhancing our understanding of the molecular bases of tree biological processes using genomic techniques. One such technique is transcriptional profiling that assays the transcript abundance of thousands of genes. The ­analyses of these inventories of gene expression help explain the genetic diversity of trees and trees’ responses to different developmental stages and environmental conditions. In this chapter, we describe key approaches for collecting transcriptome data and the tree genomic resources available for this data’s use and interpretation. We define the factors that cause gene transcript abundances to vary and elucidate how to quantify these factors’ effects. We also describe approaches to identify co-regulated genes and to assign functions to genes and groups of genes. Finally, we suggest future directions for tree transcriptome analyses.

Keywords

Bioinformatics Expression analysis Microarray High-throughput sequencing Transcriptome Gene expression variation Gene co-regulation Functional annotation 

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© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Plant AgricultureUniversity of GuelphGuelphCanada

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