Copy Number Determination: Results

Based on the eleven independent measurements in this study, the correlation coefficient between pair-wise measurements was calculated. The overall correlation between a given measurement and all other measurements was estimated by its mean correlation coefficient (Fig. 1). Most of the measurements highly correlated with each other, with a mean correlation coefficient more than 0.91. Only 2 measurements, with the lowest genomic DNA amount (40 ng) and lowest total RNA amount (3 mg), respectively, have a lower mean correlation coefficient (0.86) and therefore were excluded from the later analyses. The final copy number of each transcript was calculated as the median of the 9 independent measurements.

As a result, we obtained the copy number for 6110 transcripts. The absolute abundance ranges from 0.1 to 137 mRNA copies/cell (Fig. 2A), with a mean of 2.4 copies/cell and a median of 1.2 copies/cell (Fig. 2B). The general trend of the copy numbers determined by cDNA microarray is in fairly good agreement with those obtained by HDA and SAGE technology, even though the absolute copy number for some transcripts may vary significantly. We also computed the transcriptome composition of functions as described by (1). As shown in Fig. 3, the transcriptome enrichment in terms of broad functional categories (MIPS) determined by cDNA microarray was highly correlated with HDA (correlation 0.97) and SAGE (correlation 0.85) results. Among the highest enriched categories are protein synthesis (376%), energy (154%) and cellular organization (58%). The metabolism category was also enriched 21% according to our data that was consistent with SAGE data (25% enrichment) but different from HDA data (depleted 10%). The most depleted categories include unclassified proteins (-100%) and transposon (-88%), although the extent of depletion was not as significant as the enrichment. Table 1 (2.88MB Excel file) summarizes the yeast transcriptome data determined by two different techniques.

References:

1. R. Jansen, M. Gerstein, Nucleic Acids Res 28, 1481-8. (2000).