15 research outputs found

    Predicted numbers of bacterial membrane, potentially surface exposed and secreted proteins as a function of the total number of proteins.

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    <p>The predicted numbers of (A) membrane (mem), (B) potentially surface exposed (pse), and (C) secreted (sec) proteins in a bacterial species are correlated to the total number of encoded proteins (Spearman's rank correlation test, p < 0.01), with the exception of the sec proteins in gut bacteria where no significant correlation is observed (p > 0.2). Red, gut bacteria; blue, non-gut bacteria.</p

    Functional clustering of bacterial species used in this study.

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    <p>Clustering of 46 species on the basis of functional profiles (presence or absence of bactNOGs). Green, gut species; Violet, non-gut species. A and B represent phylogenetically distinct clusters (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159030#pone.0159030.g001" target="_blank">Fig 1</a>).</p

    Phylogeny of bacterial species used in this study.

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    <p>16S rRNA based tree by Maximum Likelihood method. Green, gut species; Violet, non-gut species. Clusters A and B make part of one functional cluster (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159030#pone.0159030.g002" target="_blank">Fig 2</a>).</p

    Distribution of functions among gut and non-gut genomes.

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    <p>Squares indicate bactNOGs as a function of the number of gut genomes (horizontal axis) and the number of non-gut genomes (vertical axis) in which they are encoded. The colours of the squares indicate the numbers of different bactNOGs at each position. BactNOGs encoded in only one of the 46 genomes are not indicated. Diagonal lines separate bactNOGs that are overrepresented in the gut genomes (bottom right), bactNOGs that are underrepresented in the gut genomes (top left), and bactNOGs with an intermediate position (see text for details).</p

    Functional composition of gut species bactNOG datasets.

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    <p>BactNOGs represented in one or more of the 23 gut bacterial species in this study were attributed to one of three groups: overrepresented or underrepresented compared to non-gut species (see text for details), or neither over nor underrepresented (indicated by *). Within each of these groups, the number of different BactNOGSs attributed to a functional category is indicated as a percentage of the total number of BactNOGs in the group. Functional category descriptions are short forms of the full descriptions presented in tables “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159030#pone.0159030.s001" target="_blank">S1</a>” and “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159030#pone.0159030.s002" target="_blank">S2</a>” Tables.</p

    Conceptually distinct classes of epi-polymorphisms.

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    <p>A) <i>Induced</i> SNEPs are defined here as inter-strain differences that arose from a stochastic or environmentally-induced epigenetic change. B) <i>DNA-encoded</i> SNEPs are genetically determined by differences in the DNA sequence. C) After individuals have undergone perturbing environmental conditions, the SNEPs initially present may be lost (called <i>labile</i>), or remain (called <i>persistent</i>).</p

    Master <i>ace</i>QTLs.

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    (i)<p>Sum of linkage posterior probabilities across all target nucleosomes.</p>(ii)<p>Based on annotations of target genes and previous <i>e</i>QTL studies <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002958#pgen.1002958-Yvert1" target="_blank">[38]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002958#pgen.1002958-Smith1" target="_blank">[47]</a>.</p>(iii)<p><i>Nae/Na</i>, where <i>Nae</i> is the number of nucleosomes targeted by this master-<i>ace</i>QTL, that are located within 10 Kb of a gene identified as an <i>e</i>QTL target of the same regulatory region; and <i>Na</i> is the total number of nucleosomes targeted by this master-<i>ace</i>QTL.</p>(iv)<p>Based on the fraction of nucleosomes matching expression targets: ‘<i>ace</i>QTL only’: less than 25%, ‘also <i>e</i>QTL’: more than 75%, ‘partial’: in between. In some cases, ‘partial’ or ‘<i>ace</i>QTL only’ could be seen despite the colocalization of a master-<i>e</i>QTL because acetylation and expression control did not act on the same target loci.</p>(v)<p>Target nucleosomes that were located within 1 Kb of each other were grouped into a single “locus”.</p
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