title: Snapshots of gene expression in rice: limitations for allelic expression imbalance determination.
abstract: In an initial investigation of differential expression of genes caused by cis-acting regulatory elements in rice, the lack of reproducibility led us to question the basic premise of allelic expression imbalance determination: namely that departures of cDNA expression ratios from those observed in genomic DNA provide unequivocal evidence of cis-acting polymorphisms. This paper describes experiments designed to demonstrate that stochastic variation in low copy number of targets in PCR reactions give variable allelic ratios even when starting with the same copy numbers of the two alleles. These significant departures from an expected 1:1 ratio provide an explanation to the lack of reproducibility observed for our cDNA measurements.
authors.affiliation: John Bingham Laboratory, National Institute of Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, UK.
authors.forename: Harika
authors.initials: H
authors.lastname: Akkinepalli
authors.forename: Nelzo
authors.initials: N
authors.lastname: Ereful
authors.forename: Yan
authors.initials: Y
authors.lastname: Liu
authors.forename: Kaye
authors.initials: K
authors.lastname: Malabanan
authors.forename: Rhian
authors.initials: R
authors.lastname: Howells
authors.forename: Konstantina
authors.initials: K
authors.lastname: Stamati
authors.forename: Wayne
authors.initials: W
authors.lastname: Powell
authors.forename: Hei
authors.initials: H
authors.lastname: Leung
authors.forename: Andy
authors.initials: A
authors.lastname: Greenland
authors.forename: Ian
authors.initials: I
authors.lastname: Mackay
authors.forename: David
authors.initials: D
authors.lastname: Lee
mesh_terms: D022981:Allelic Imbalance; D018628:Gene Dosage; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012045:Regulatory Sequences, Nucleic Acid