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D. Choi, Y. Fang, W.D. Mathers; Gene Ontology of Abundant Transcriptomes in Mouse Lacrimal Gland Using cDNA Microarray Technology . Invest. Ophthalmol. Vis. Sci. 2006;47(13):4909.
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© ARVO (1962-2015); The Authors (2016-present)
To explore whether cDNA microarrays can be used to identify abundant transcriptomes in the mouse lacrimal gland and their gene ontology analysis.
From our previous cDNA microarray data, the total RNA of the lacrimal glands of control and cornea–burned mice was hybridized with NIA 15K cDNA microarrays, and we extracted normalized gene expression levels of control mice. The data included 16 Type A (8400A) and 16 Type B (6600A) arrays containing 4 pooled biological samples, each had 4 technological replicates, respectively. Within each array, gene expressions were converted into percent ranks and then averaged across the same type of arrays. The abundant transcriptomes were annotated and their gene ontology was analyzed by NIH David v1.0. (http://apps1.niaid.nih.gov/david/)
Within each type of array, the correlations across arrays were high, at least 0.8. The higher percent ranked transcriptomes, especially those with average percent ranks over 80%, had considerably smaller standard deviation and consistent percent ranks than others. The updated annotation from Standford Source showed there were many unknown genes even in the top 20% of the transcriptome, with 39.1% (634/1623) unknown genes in Type A and 39.2% (530/1352) in Type B. Gene ontoloies for the top 20% transcriptomes of each array type(type A: 1623, type B: 1352) were analyzed using NIH David database. The major categories of gene ontology by biological function were cell growth and maintenance, protein metabolism, biosynthesis, and nucleic acid metabolism, while purine nucleotide binding, DNA and RNA binding, and hydrolase activity were major categories by molecular function. However, when the most abundant transcriptomes were compared to the results in Ozyildirim et al (IOVS, May 2005, Vol. 46, No. 5, pp1572–1580), there was little overlap.
Discussion and Conclusions: :
The two–channel cDNA microarray technology is not designed to quantitate transcriptomes or to compare their abundance. Our abundant gene list may reveal, instead, the relative efficiency of hybridization between the probes and the RNA, the amount of spotted material on the chip, or other factors. The low standard deviations of apparently abundant genes may reflect saturation of the spots.
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