reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat
Extracts half-lives of RNAs from Supplementary Table S4 of Chen et al., “Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli” (2014) and Supporting Table 5 of Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichi coli at single gene resoluation using two-color fluorescent DNA microarrays” (2002). Optionally generates a comparison plot for degradation rates reported for the same gene from these two sources.
- reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.build_half_life_table(chen_half_lives, bernstein_half_lives, all_gene_ids)[source]
Builds the RNA half-life flat file that is used as raw_data for the simulation using the data from the two papers. If data for a gene exists in both papers, we use data from Chen et al. assuming that their methodology is more accurate. In the output file monocistronic RNAs (represented by their corresponding gene IDs) are listed first, followed by polycistronic RNAs.
- reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.compare_half_lives(chen_half_lives, bernstein_half_lives)[source]
Generates a scatter plot that compares the half-lives of RNAs reported in both Chen et al. and Bernstein et al.
- reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.get_bernstein_half_lives(symbols_to_ids)[source]
Reads RNA half lives reported by Bernstein et al., and stores them in a dictionary. Any gene listed that does not exist in the model are skipped. Bernstein et al. only reports half-lives of monocistronic RNAs.
- reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.get_chen_half_lives(symbols_to_ids)[source]
Reads RNA half lives reported by Chen et al., and stores them in a dictionary. Any gene/transcription unit listed that does not exist in the model are skipped.