Supporting information for Arava et al. (2003) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0635171100
Fig. 8.
Analysis of the correlation between ORF length and ribosome density for various mRNA subsets. We have analyzed the correlation between the ORF length and ribosome density for several functional subsets. (A) mRNAs encoding for ribosomal proteins (RP). To ensure that the inverse correlation does not arise from the effects of a small subset of highly expressed genes, we excluded from the analysis the genes encoding for ribosome-associated proteins (Left). The correlation is still apparent with a Spearman rank of –0.78. The complementary analysis, looking only at the genes encoding for the ribosome-associated proteins (Right) also reveals the correlation. The mRNAs encoding ribosomal proteins are relatively short and sediment at the well resolved region of the gradient (<5 ribosomes). (B) mRNAs encoding proteins localized in the mitochondria. Correlation analysis was performed within the group of mRNAs encoding for mitochondrial protein (taken from Yeast Proteome Database, July 2000 release). The high inverse correlation is still apparent. (C) mRNAs cosedimenting with the mitochondria. Correlation analysis was performed within a group of mRNAs reported to be closely associated with the mitochondria [Marc, P., Margeot, A., Devaux, F., Blugeon, C., Corral-Debrinski, M. & Jacq, C. (2002) EMBO Rep. 3, 159–164]. For the analysis, only mRNAs reported to have mitochondrial localization of mRNA (MLR) >80 were taken. (D) mRNAs associated with membrane fractions. Correlation analysis was performed within a group of mRNAs reported to be associated with membranes [Diehn, M., Eisen, M. B., Botstein, D. & Brown, P. O. (2000) Nat. Genet. 25, 58–62]. For the analysis, only mRNAs reported to have ratios >2 were taken.