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Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences

Show simple item record Su, Wan-Lin en_US Modrek, Barmak en_US GuhaThakurta, Debraj en_US Edwards, Stephen en_US Shah, Jyothi, K. en_US Kulkarni, Amit V. en_US Russell, Archie en_US Schadt, Eric E. en_US Johnson, Jason M. en_US Castle, John C. en_US 2010-05-06T20:05:28Z 2010-05-06T20:05:28Z 2008 en_US
dc.identifier.citation Su W, Modrek B, GuhaThakurta D, et al. Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences. BMC Genomics. 2008;9(1):273. en_US
dc.identifier.other 10.1186/1471-2164-9-273 en_US
dc.identifier.uri en_US
dc.description.abstract Background: Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays to establish the extent of variation found in mouse strains and genders. Here, we surveyed the effect of strain and sex on liver gene and exon expression using male and female mice from three different inbred strains. Results: 71 liver RNA samples from three mouse strains - DBA/2J, C57BL/6J and C3H/HeJ - were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon probe ("3' gene expression profiling") and using all probes associated with the gene ("whole-transcript gene expression profiling"), while exon expression was determined using exon probes and flanking junction probes that spanned across the neighboring exons ("exon expression profiling"). Widespread strain and sex influences were detected using a two-way Analysis of Variance (ANOVA) regardless of the profiling method used. However, over 90% of the genes identified in 3' gene expression profiling or whole transcript profiling were identified in exon profiling, along with 75% and 38% more genes, respectively, showing evidence of differential isoform expression. Overall, 55% and 32% of genes, respectively, exhibited strain- and sex-bias differential gene or exon expression. Conclusion: Exon expression profiling identifies significantly more variation than both 3' gene expression profiling and whole-transcript gene expression profiling. A large percentage of genes that are not differentially expressed at the gene level demonstrate exon expression variation suggesting an influence of strain and sex on alternative splicing and a need to profile expression changes at sub-gene resolution. en_US
dc.language.iso en_US en_US
dc.title Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences en_US
dc.type Article en_US

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