Additional file 6: Figure S4.
Upstream open reading frames (uORFs) and longer coding sequences contribute to poor translatability of mRNAs in rpl24b and eif3h mutants. The contribution of the length of main open reading frame (ORF or CDS) and the presence of uORFs to the translation state (TL) of mRNAs. mRNAs were classified into bins according to differences in translation state (Δlog2 TL) between rpl24b and wild-type (A) or eif3h and wild-type (B). Each bin was evaluated for the percentage of genes falling into three classes (i) genes harboring uORFs; (ii) genes lacking uORFs but having a long (>1,086 nt) ORF; (iii) genes lacking uORFs but with a short (<1,086 nt) ORF. The number of genes in each class is indicated. The 2 × 2 contingency tables were prepared from the 'no change’ bin (> - 0.2 Δlog2 TL <0.2), and each of the other bins. Fisher’s exact test (or χ2 test with Yates’ correction for the larger classes) was carried out using these tables to evaluate the extent of deviation of each bin from the 'no change’ bin. Significant (>0.0001 P <0.05) and highly significant (P <0.0001) deviations are shown with single and double asterisks, respectively. (C) mRNAs that depend specifically on eIF3h are strongly enriched for uORFs, while mRNAs that depend on both eIF3h and RPL24B are not.
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Tiruneh et al. BMC Biology 2013 11:123 doi:10.1186/1741-7007-11-123