Additional file 1 of PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures

Supplementary Methods. Detailed mathematical description of the methods underlying patteRNA. (PDF 233 kb

Additional file 2 of PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures

Supplementary Figures and Tables. (PDF 7600 kb

Additional file 3 of PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures

Reviewer reports and author’s response to reviewers. (DOCX 28 kb

Automated recognition of RNA structure motifs by their SHAPE data signatures

<p>Datasets, code and results supporting the manuscript:</p> <p>Radecki P., Ledda M. & Aviran S., Automated recognition of RNA structure motifs by their SHAPE data signatures</p

Genome- and metabolome-wide analysis results, first stage.

<p>(A) Manhattan plot for feature 1.2025. (B) Genome- and metabolome-wide P-value heat map, showing associations with <i>P_C</i><5×10⁻⁸ in <i>CoLaus</i>. (C) Pseudo-spectrum for SNP rs37369, obtained by plotting the association P-values between rs37369 and all metabolic features.</p

Allelic heterogeneity at the <i>AGXT2</i> locus.

<p>Abbreviations: <i>P_C, P_T</i> – P-values, <i>x_C, x_T</i> – multivariate effect sizes, <i>R²</i> – explained variance of full model, <i>R²_diff</i> – additional explained variance of full model compared to best single SNP association, <i>model P</i> – probability of observing same or equal <i>R²_diff</i> increase with the same stepwise model selection for 2,500 permuted phenotypes.</p

Local Manhattan plots.

<p>The Manhattan plots show combined −log(P-values) in the neighborhood of the most strongly associated SNP for (A) the <i>FUT2</i> with fucose association, and (B) the <i>SLC7A9</i> with lysine association.</p

Metabomatching.

<p>Each subfigure compares the <i>CoLaus</i> pseudo-spectrum (bottom half) with the NMR spectrum (top half) of the most likely candidate for the associated metabolite. (A) rs37369 vs. 3-aminoisobutyrate. (B) rs2147896 in <i>PYROXD2</i> vs. trimethylamine (C) rs8101881 in <i>SLC7A9</i> vs. lysine (D) rs281408 in <i>FUT2</i> vs. fucose.</p

Locus-metabolite associations.

<p>For every locus, the association results are listed for the strongest association, after meta-analysis, of a SNP in the locus with a feature (bold) of the metabolite. Abbreviations: Chr – chromosome, Position – chromosomal position in NCBI build 36, <i>x_C</i> – effect size in <i>CoLaus</i>, <i>x_T</i> – effect size in <i>TasteSensomics</i>, <i>x_m</i> – effect size after meta-analysis, <i>P_m</i> – P-value after meta-analysis.</p

Genotype-Metabotype-Phenotype associations.

<p>The two novel gene-metabolite associations of this study implicate SNPs that had previously been associated with disease-related phenotypes by the indicated publications: (A) Fucose–Crohn's disease–<i>FUT2</i> (rs492602), (B) Lysine–eGFR–<i>SLC7A9</i> (rs8101881). A link between the metabolite and the phenotype has been established for (A) based on a mouse model and for (B) by a direct correlation with the indicated significance and effect size. Abbreviations: OR refers to the odds ratio, <i>x</i> to the linear regression effect size, <i>P</i> to the corresponding P-value, and the <i>m</i>-index indicates values obtained in the combined <i>CoLaus</i> and <i>TasteSensomics</i> sample.</p