The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape.

BMC Plant Biology
D Marc JonesRichard J Morris

Abstract

Transcriptome time series can be used to track the expression of genes during development, allowing the timing, intensity, and dynamics of genetic programmes to be determined. Furthermore, time series analysis can reveal causal relationships between genes, leading to an understanding of how the regulatory networks are rewired during development. Due to its impact on yield, a developmental transition of agricultural interest in crops is the switch from vegetative to floral growth. We previously reported the collection of genome-wide gene expression data during the floral transition in the allopolyploid crop Brassica napus (oilseed rape, OSR). To provide the OSR research community with easy access to this dataset, we have developed the Oilseed Rape Developmental Expression Resource (ORDER; http://order.jic.ac.uk ). ORDER enables users to search for genes of interest and plot expression patterns during the floral transition in both a winter and a spring variety of OSR. We illustrate the utility of ORDER using two case studies: the first investigating the interaction between transcription factors, the second comparing genes that mediate the vernalisation response between OSR and radish (Raphanus sativus L.). All the data is downloa...Continue Reading

References

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

BLAST
AionPlot
jQuery
Cufflinks
js
MongoDB
Ensembl
D3
ORDER
Bootstrap

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