Network Dynamic Analysis Figure 4. A time-delay effect from transcription rate data to mRNA abundance data. A) Correlation matrix between time points for mRNA abundance (RA) and transcription rate (TR) analysis under an osmotic stress condition is shown; B) Only correlations between TR and RA shown. doi:10.1371/journal.pone.0009908.g004 Next, we examined whether transcription rate or steady-state mRNA abundance is a better measurement of functional relatedness between two genes. D.1. Co-occurrence in the same operon by bacterial orthologs indicates functional relatedness between S. cerevisiae genes. Co-occurrence in the same operon (co- operon) by the two genes in bacterial genomes indicates functional relatedness; such genes often participate in the same biochemical pathways [24]. We tested whether two S. cerevisiae genes are functionally related when their bacterial orthologs putatively co-occur in the same operon (see Materials and Methods). Figure 5 displays the distributions of pair-wise correlation coefficients for yeast gene pairs whose bacterial orthologs display a co-operon frequency of one or more. When compared with the distributions in figures 1 and 2, significant positive correlation coefficients were substantially enriched. As discussed earlier (see Results section A), the mass of the distribution shifted to the right, dramatically enlarging the positive correlation peak. Significant negative correlations were substantially reduced; the peaks corresponding to negative correlation coefficient were severely reduced when compared with the corresponding peaks in figures 1 and 2. Thus, having their bacterial orthologs sharing an operon strongly indicated functional relatedness between two S. cerevisiae genes. D.2. Transcription rate correlates better with co-operon frequency. In order to compare transcription rate and mRNA abundance as measurement of functional relatedness, we need an independent measurement of functional relatedness to compare the Figure 5. Co-occurrence in the same operon by their bacterial orthologs indicates functional relatedness between S. cerevisiae genes. Distribution of correlations between genes whose bacterial orthologs co-occur in the same operon at least once are shown; A) data for mRNA abundance levels; B) data for transcription rates. doi:10.1371/journal.pone.0009908.g005 PLoS ONE | www.plosone.org 5 March 2010 | Volume 5 | Issue 3 | e9908