Skip to main content
Article thumbnail
Location of Repository

Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

By Neil S. Graham, Martin R. Broadley, John P. Hammond, Philip J. White and Sean T. May


Background: Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We\ud have previously developed a technique to study the transcriptomes of heterologous species based\ud on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology.\ud Results: Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation\ud intensity increased the number of genes identified as significantly differentially expressed in two\ud published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice.\ud Conclusion: This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays

Topics: QR
Publisher: BioMed Central Ltd.
Year: 2007
OAI identifier:

Suggested articles


  1. (2005). A gene expression map of Arabidopsis development. doi
  2. (2003). Aldape KD: A model of molecular interactions on short oligonucleotide microarrays. Nature Biotechnology doi
  3. (2005). Close TJ: Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during vegetative growth stage. Plant Physiology doi
  4. (2004). Comparitive microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotinamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. doi
  5. (2004). Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. doi
  6. (1999). DJ: High density synthetic oligonucleotide arrays. Nature Genetics doi
  7. (2003). Elevated gene expression levels distinguish human from non-human primate brains. doi
  8. (2003). Gruissem W: Arabidopsis transcript profiling on Affymetrix GeneChip arrays. Plant Molecular Biology doi
  9. (2002). Head SR: Analysis of results variability from highdensity oligonucleotide arrays comparing same-species and cross-species hybridisations. Biotechniques
  10. (2006). Hoffman EP: Probe-set algorithms: Is there a rational best bet? BMC Bioinformatics
  11. (2004). Irizarry RA: Reprocessing of oligonucleotide array data. doi
  12. (2005). JA: BarleyBase – An expression profiling database for plant genomics. Nucleic Acids Research
  13. (2005). JGN: In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip® technology. BMC Genomics
  14. (2000). Large scale profiling of the Arabidopsis transcriptome. Plant Physiology doi
  15. (2004). Paabo S: A neutral model of transcriptome evolution. doi
  16. (2002). Paabo S: Intra- and interspecific variation in primate gene expression patterns. Science
  17. (2004). S: A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Research doi
  18. S: NASCArrays: A repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Research doi
  19. (2004). Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. doi
  20. (2003). Speed TB: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics
  21. ST, Broadley MR: A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. New Phytologist doi
  22. ST: Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. Plant Methods
  23. (2003). TA: Probe selection for high-density oligonucleotide arrays. doi
  24. (2003). TP: Gene expression analysis of the acute phase response using a canine microarray. Toxicological Sciences doi
  25. (2005). W-R: Genome-wide identification of superior reference genes for transcript normalisation in Arabidopsis. Plant Physiology doi
  26. (2001). Wong WH: Model-based analysis of oligonucleotide arrays: design issues and standard error application. Genome Biology
  27. (2001). Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. doi
  28. Xspecies .cel file parser Version

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.