Additional file 5 of Complex regulation of ADAR-mediated RNA-editing across tissues

Figure S5. A-to-I editing frequency at 575 sites across nineteen tissue samples, represented as a heatmap. These sites were selected on the basis of having at least 10X coverage and an editing frequency >0.4 in at least one tissue. Tissues for which the coverage was < 10X at a site appear as cyan. Very few sites are highly edited across all nine tissues. Most sites that are edited in only one tissue are often not expressed (insufficient read coverage) in the other tissues. (PDF 373 kb

Additional file 7 of Complex regulation of ADAR-mediated RNA-editing across tissues

Figure S7. The variability in editing frequency per site across tissues in the human Illumina Body Map 2 dataset. Only samples with ≥ 10X coverage at these sites are plotted. Three sites where the RDD encodes a non-synonymous change were selected and presented here (Tmem63b, Flnb, and Copa). (PDF 5 kb

Additional file 1 of Complex regulation of ADAR-mediated RNA-editing across tissues

Figure S2. The ratio of reads mapping to introns versus exons in each sample. (PDF 5 kb

Neighbor-Joining Trees Summarizing Proteome-Wide Trends in Protein Similarity and Genome-Wide Trends in Intron–Exon Structural Similarity

<p>Proteome-wide trends in protein similarity (A), and genome-wide trends in intron–exon structural similarity (B). Numbers beneath tree nodes are bootstrap values.</p

D. melanogaster Intron Lengths Are Highly Correlated with Their Inferred D. pseudoobscura Orthologs; D. melanogaster Paralogous Introns Show No Such Correlation

<p>(A) <i>x</i>-axis, length (log₁₀) of annotated D. melanogaster introns; <i>y</i>-axis, length (log₁₀) of their inferred orthologs in the D. pseudoobscura genome. Red circles indicate those introns containing a transposon in <i>D. melanogaster;</i> blue circles indicate those introns containing a transposon in <i>D. pseudoobscura;</i> gold circles indicate introns without identifiable transposons in either species. Spearman correlation coefficient: 0.637; <i>p</i> < 0.001.</p> <p>(B) Intron lengths of paralogs having the same intron–exon structure as judged by the positions of their splice junctions relative to the protein alignments of their reciprocal best-hit best HSPs. <i>x</i>-axis, length (log₁₀) of introns in an annotated D. melanogaster gene; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns. Spearman correlation coefficient: 0.448; <i>p</i> < 0.001.</p

Cumulative Distribution Functions Illustrating Proteome-Wide Trends in Protein Similarity

<p><i>x</i>-axis, bits/aligned position; <i>y</i>-axis, cumulative fraction of HSPs having that number of bits/aligned amino acid pair or less. To facilitate display, only a subset of the 21 possible pair-wise combinations is shown. Data are based upon all reciprocal best BLASTP hits identified in all versus all BLASTP searches of the proteomes. Similarity calculations were restricted to the high-scoring HSP for each BLAST hit, in order to avoid data duplication due to overlapping alignments.</p> <p>There were 13,339 <i>M. musculus–H. sapiens</i> reciprocal best hits; 6,435 between D. melanogaster and <i>A. gambiae;</i> 5,828 between C. intestinalis and <i>H. sapiens;</i> 5,542 between D. melanogaster and <i>H. sapiens;</i> 4,669 between C. elegans and <i>H. sapiens;</i> 4,588 between C. elegans and <i>D. melanogaster;</i> 3,361 between H. sapiens and <i>A. thaliana;</i> and 2,835 between C. elegans and A. thaliana.</p> <p>atha, <i>A. thaliana;</i> cele, <i>C. elegans;</i> cint, <i>C. intestinalis;</i> dmel, <i>D. melanogaster;</i> hsap, <i>H. sapiens;</i> mmus, <i>M. musculus.</i></p

Intron Lengths Can Be Used as a Molecular Clock

<p><i>y</i>-axis, magnitude of the Spearman correlation coefficient for the five <i>Drosophila</i> distributions shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-g008" target="_blank">Figure 8</a>. <i>x</i>-axis, time (millions of years) since last common ancestor based on protein similarities as calculated in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-b030" target="_blank">30</a>]. Black bars above and below each data point denote observed variance in the data and were obtained by randomly resampling 1,000 orthologous intron pairs 100 times. Best-fitting curve (shown in black) y = −0.0057x + 0.9266; R² = 0.9875.</p

Controlling for the Impact of Unequal Rates of Protein Evolution on the Evolution of Intron–Exon Structures

<p>(A) Unrooted neighbor-joining tree based upon amino acid similarities for reciprocal best-hit best HSPs having 1.25 bits/aligned amino acid pair.</p> <p>(B) Unrooted neighbor-joining tree based upon similarities in the intron–exon structures of those same HSPs.</p

Global Overview of Gene Structure in Six Annotated Animal Genomes

<p>(A) Intron length. Annotated intron length (log₁₀) is plotted on the <i>x</i>-axis; the frequency at which introns of that length occur in an organism's genome is plotted on the <i>y</i>-axis.</p> <p>(B) Exon length. <i>x</i>-axis, coding-exon length in nucleotides; <i>y</i>-axis, frequency.</p> <p>(C) Intron density. A transcript's intron density is equal to its number of coding introns divided by the length of the protein it encodes. <i>y</i>-axis, frequency of annotated transcripts with a particular intron density. <i>x</i>-axis, intron density binned in increments of 0.5 introns/100 amino acid (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#s4" target="_blank">Materials and Methods</a>). Deuterostomes are shown in shades of blue; protostomes in shades of red.</p