Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2017 Jan 31;6:e22037. doi: 10.7554/eLife.22037

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 2017, Burkhardt et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

PMC Copyright notice

Figure 3. — (A) Plots comparing the Gini indices of ORFs in polycistronic operons calculated from in vivo DMS-seq to their TEs (N = 483). (B) Histograms of TE ratios between adjacent non-overlapping (N = 253) or overlapping (N = 73) ORFs in operons (see Materials and methods for details). Overlapping ORFs are ORF pairs for which the annotated stop codon of the upstream ORF overlaps or is 3’ of the start codon of the downstream ORF. (C–E) Plots comparing the Gini indices of endogenous ORF mRNAs calculated from DMS-seq data of: C. in vivo RNA; D. in vivo RNA with no translating ribosomes (Ksg treated cells); E. in vitro modified refolded mRNA, to their TEs. For this and all subsequent panels, data calculated using different sets of ORFs are summarized in Supplementary file 1–3. (F) Plot comparing computationally predicted mRNA structure (- minimum free energy / nucleotide; -ΔG/nt) of the entire ORF body to TE. (G) Plots of the difference in the Gini index between untranslated (ksg-treated) and translated in vivo mRNA against their TE for the 465 ORFs in both datasets. X-axis: Gini index (in vivo untranslated) – Gini index (in vivo), normalized by the average of the two.

DOI: http://dx.doi.org/10.7554/eLife.22037.006

Figure 3—figure supplement 1. — (A) Plots comparing the Gini indices of ORFs in polycistronic operons calculated from in vivo DMS-seq to their TEs (N = 483). (B) Histograms of TE ratios between adjacent non-overlapping (N = 253) or overlapping (N = 73) ORFs in operons (see Materials and methods for details). Overlapping ORFs are ORF pairs for which the annotated stop codon of the upstream ORF overlaps or is 3’ of the start codon of the downstream ORF. (C–E) Plots comparing the Gini indices of endogenous ORF mRNAs calculated from DMS-seq data of: C. in vivo RNA; D. in vivo RNA with no translating ribosomes (Ksg treated cells); E. in vitro modified refolded mRNA, to their TEs. For this and all subsequent panels, data calculated using different sets of ORFs are summarized in Supplementary file 1–3. (F) Plot comparing computationally predicted mRNA structure (- minimum free energy / nucleotide; -ΔG/nt) of the entire ORF body to TE. (G) Plots of the difference in the Gini index between untranslated (ksg-treated) and translated in vivo mRNA against their TE for the 465 ORFs in both datasets. X-axis: Gini index (in vivo untranslated) – Gini index (in vivo), normalized by the average of the two.

DOI: http://dx.doi.org/10.7554/eLife.22037.006