Abstract
BackgroundAffymetrix 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 have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology.ResultsHere 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 intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice.ConclusionThis mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.
Highlights
Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species
Genomic DNA hybridisations and probe selection The aim of the study was to investigate the effects of using a mixed physical and bioinformatics probe-masking approach on the study of the transcriptomes of two species
Arabidopsis thaliana and rice genomic DNA (gDNA) was hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively
Summary
Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. BMC Genomics 2007, 8:344 http://www.biomedcentral.com/1471-2164/8/344 match (MM) probe, which contains a mis-match base at the 13th base position, designed to measure non-specific binding [1] This contrasts with the single cDNA or oligo probe used to assay a gene on most other arrays. Other normalisation algorithms have been developed that use the signal intensities from all the arrays in an experiment to determine gene expression values These include "ModelBased Expression Indexes" [9,10] and the "Robust Multiarray Average" (RMA) algorithms [11]. With these methods, the probe response pattern across all genes is fitted across all the arrays used in an experiment and a robust estimate of the background signal is modelled and the data adjusted . Examples of these models are "Positional-Dependent-Nearest-Neighbour model" [12] and GC-RMA [13]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
