Using human microarrays to identify differentially expressed genes associated with increased steroidogenesis in boars.
Human microarrays are readily available, and it would be advantageous if they could be used to study gene expression in other species, such as pigs. The objectives of this research were to validate the use of human microarrays in the analysis of porcine gene expression, to assess the variability of the data generated, and to compare gene expression in boars with different levels of steroidogenesis. Cytochrome b5 (CYB5) expression was used to assess array detection sensitivity. Samples having high or low CYB5 RNA levels were hybridized to microarrays to determine if the known expression difference could be detected. Six hybridizations were conducted using human microarrays containing 3840 total spots representing 1718 characterized human ESTs. To analyze gene expression in boars with different levels of steroidogenesis, testis RNA from four boars with high levels of plasma estrone sulphate was hybridized to testis RNA from four boars with lower levels. Eight microarray hybridizations were conducted including fluor-flips. Self-self hybridizations were also conducted to assess the variability of array experiments. The Cy5 and Cy3 intensity values for each array were normalized using a locally weighted linear regression (LOESS). Statistical significance was assessed using a Student's t-test followed by the Benjamini and Hochberg multiple testing correction procedure. Quantitative real-time PCR (Q-RT-PCR) was used to verify select gene expression differences. The results show that CYB5 was significantly overexpressed in the high CYB5 sample by 1.8 fold (P < 0.05), verifying the known expression difference. The average log2 ratio of the majority of genes (1643) falls within one standard deviation of the mean, indicating the data were reproducible. In the high versus low steroidogenesis experiment, seven genes were significantly overexpressed in the high group (P < 0.05). Quantitative real-time PCR was used to validate five genes with the highest fold change, and the results corroborated those found by the microarray experiments. The results of the self-self hybridizations showed that no genes were significantly differentially expressed following the application of the Benjamini and Hochberg multiple testing correction procedure. The results presented in this report show that human arrays can be used for gene expression analysis in pigs.
Stewart
Jennifer D
JD
Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada.
Lou
Yanping
Y
Squires
E James
EJ
Coussens
Paul M
PM
D000818:Animals; D002232:Carbocyanines / Q000737:chemistry; D015786:Cytochromes b5 / Q000096:biosynthesis / Q000235:genetics; D004970:Estrone / Q000031:analogs & derivatives* / Q000096:biosynthesis / Q000097:blood / Q000235:genetics; D005456:Fluorescent Dyes / Q000737:chemistry; D015971:Gene Expression Regulation, Enzymologic; D006801:Humans; D008297:Male; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary*; D012313:RNA / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000662:veterinary; D013552:Swine / Q000235:genetics* / Q000378:metabolism; D013737:Testis / Q000378:metabolism
D002232:Carbocyanines; D005456:Fluorescent Dyes; C089187:cyanine dye 3; C085321:cyanine dye 5; D004970:Estrone; D012313:RNA; D015786:Cytochromes b5; C017296:estrone sulfate