Populations enriched for hematopoietic stem cells.

<p>Populations enriched for hematopoietic stem cells.</p

Bone marrow stromal cell types (endosteal) known to contribute to the hematopoietic microenvironment.

<p>Bone marrow stromal cell types (endosteal) known to contribute to the hematopoietic microenvironment.</p

Bone marrow stromal cell types (vascular/endothelial) known to contribute to the hematopoietic microenvironment.

<p>Bone marrow stromal cell types (vascular/endothelial) known to contribute to the hematopoietic microenvironment.</p

Detailed curation of an interaction in HSC-Explorer.

<p>Information about the interaction between ‘Tie2/Ang1 signaling’ and the term ‘quiescence’ consists of (a) ‘General information’ about the organism used in the experiment and reference, (b) textual information (‘Comment’) about the interaction and experimental procedure, and (c) structured information including in addition information about the hematopoietic cell-type.</p

<i>AGXT2</i> pseudospectrum and 3-aminoisobutyrate NMR spectrum, descriptions, and metabomatching match sets.

<p>(A) The upper plot shows the experimental NMR spectrum of 3-aminoisobutyrate. The lower plot shows the (-log) <i>p</i>-values of the pseudospectrum of rs37369 in <i>AGXT2</i>, when <i>p</i> < 10⁻³. There is a close match between the experimental spectrum and the pseudospectrum, as the four sets of features that associate (<i>p</i> < 5 × 10⁻⁸) with rs37369 correspond to the principal peaks of the spectrum. (B) Taking a more detailed view of the spectrum descriptions (from HMDB), we see that the peaks of 3-aminoisobutyrate group into six clusters (labeled A through F). The multiplet ranges for clusters A, C, and E enclose their corresponding peaks well, padding by an average of 0.023 ppm. The multiplet range for cluster F is significantly wider, padding by 0.062 ppm. Approximating cluster areas as the product of the width of the cluster with the average height of the peaks in the cluster, then scaling, we find area-derived proton counts of 2.8, 0.7, 1.1, 1.2 for clusters A, C, E, and F, respectively. These counts are coherent with the listed proton counts of 3, 1, 1, and 1 for the respective multiplet ranges. Applying this same approximation for clusters B and D results in area-derived proton counts of 0.0, and 0.2. Because this implies corresponding multiplet proton counts of 0, we may consider the two spectrum descriptions essentially coherent, even though no multiplet ranges are listed for clusters B and D. (C) Match sets obtained from the peak and multiplet descriptions of the 3-aminoisobutyrate spectrum, for features resulting from a uniform NMR spectrum binning in 0.01 ppm increments, and with neighborhood parameter <i>δ</i> = 0.03 and 0.01, respectively. While the peak and multiplet descriptions of the 3-aminoisobutyrate NMR spectrum may be essentially coherent, their resulting match sets do differ, with 22 features unique to either one of the match sets.</p

CoLaus metabomatching results.

<p>Ranks of reference metabolites obtained for CoLaus pseudospectra, with UMDB as the spectral reference database, and with: peak- (P) or multiplet-mode (M), <i>χ</i>²- (X) or <i>Z</i>-scoring (Z), and without (C) or with decorrelation (D). Neighborhood parameter is <i>δ</i> = 0.03 in peak-mode, 0.01 in multiplet-mode. Shrinkage parameter is λ = 0.5 for decorrelation, 1 without. Reference metabolites are obtained from testable associations collected from targeted mGWAS [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.ref008" target="_blank">8</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.ref018" target="_blank">18</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.ref019" target="_blank">19</a>]. Squares (□) indicate ranks not in the top 10% of UMDB listed metabolites, that is ranks greater than 18. Individual metabomatching figures including the eight highest ranked metabolite candidates for each pseudospectrum can be found in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.s004" target="_blank">S1 Fig</a>. Due to the differences in the peak and multiplet descriptions, the association of the <i>HPD</i> SNP with <i>α</i>-hydroxyisobutyrate is testable only in peak mode (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.s004" target="_blank">S1F Fig</a>), the association with 3-hydroxyisovalerate only in multiplet mode (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.s004" target="_blank">S1G Fig</a>).</p

Metabomatching results on simulated metabolomes.

<p><b>A.</b> Metabomatching performance, measured as , the 90^th percentile of 1 000 ranks obtained for <i>m</i> by metabomatching pseudospectra build from the association with <b><i>M</i></b>⁰, for <i>β</i> = 0.2 (filled dots) and <i>β</i> = 1.6 (empty dots), as a function of the size of the metabolite spectrum.For <i>β</i> = 0.2, the correlation between and <i>s</i>^<i>m</i> is −0.71, with <i>p</i> ∼ 10⁻²⁶. <b>B.</b> As in (<b>A</b>), but for metabolome <b><i>M</i></b>^<i>α</i>, with <i>β</i> = 1.6, <i>N</i>_<i>a</i> = 64 and <i>α</i> = 0.6. <b>C.</b> For UMDB and <i>δ</i> = 0.02, number of match sets (<i>η</i>) that contain each feature (uniform binning in 0.01 ppm increments). <b>D.</b> Metabomatching performance, measured as , for <b><i>M</i></b>^<i>α</i>, with <i>β</i> = 1.6, <i>N</i>_<i>a</i> = 64 and <i>α</i> = 0.6, as a function of <i>η</i> of the leading peak of the metabolite spectrum, that is the peak with <i>h</i>_<i>j</i> = 1. Metabolite sizes are rounded. For <i>s</i>^<i>m</i> = 1, 2, and 3, respectively, correlations <i>ρ</i> are 0.86, 0.79, and 0.76, with <i>p</i>-values ∼10⁻¹⁰, 10⁻⁴, and 10⁻⁴.</p

SHIP metabomatching results.

<p>Metabomatching ranks of reference metabolites obtained for SHIP pseudospectra, with UMDB as the spectral reference database, and with: peak- (P) or multiplet-mode (M), <i>χ</i>²- (X) or <i>Z</i>-scoring (Z), and without (C) or with decorrelation (D). Neighborhood parameter is <i>δ</i> = 0.03 in peak-mode and 0.01 in multiplet-mode. Shrinkage parameter is λ = 0.5 for decorrelation, 1 without. Ranks obtained with 2-compound metabomatching are shown in bold, those obtained with ±-2-compound metabomatching in bold and italic. Squares (□) indicate ranks not in the top 10% of UMDB listed metabolites, that is ranks greater than 18. Individual metabomatching figures including the eight highest ranked metabolite candidates for each pseudospectrum can be found in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005839#pcbi.1005839.s005" target="_blank">S2 Fig</a>.</p

Hierarchical cluster of the correlation across 43 overlapping metabolites from both platforms.

<p>Upper colour bars represent metabolites with mGWAS results, metabolite type, and metabolite platform. The left colour bar represents the heritability of the metabolite from red (high) to white (low).</p

mGWAS results at 7 loci associated with metabolites in both platforms.

<p>mGWAS results at 7 loci associated with metabolites in both platforms.</p