Organization of the Autonomic Nuclei in the Spinal Cord : Functional Morphology

Disease-associated genes. Complete list of the disease-associated genes for each dataset. (XZ 46 kb

Communities in β’s.

<p>(A) Histogram of total number of communities detected in each network, for the 3 algorithms. Frequency is given out of the 10⁴ β’s studied here. (B) Average occurrence of community-sizes. An occurrence of 10⁻⁴ means that this community-size appeared only in 1 β out of the 10,000 studied here and an occurrence of 1 means that on average each β has one community with this size. Insert show the occurrence of sizes > 30. (C) Average number of communities detected vs. number of observed compotype species shows no correlation. Vertical bars mark standard deviation. (D) Histogram of the size of assigned communities, when a community is assigned to a compotype based on eigenvector similarity (see section: Compotype-community assignment). Mean and standard deviation are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.t001" target="_blank">Table 1</a>.</p

Box plots of compositional similarity, for the three community detection algorithms (Louvain, top; Infomap, middle; OSLOM, bottom).

<p>Similarity was measured in three cases: ‘<i>Original</i>’, when comparing the original compotype observed vs. the one in GARD under β* of its assigned community; ‘<i>Assigned</i>’, when comparing the compotype observed in a GARD simulation with β* of its assigned community to the eigenvector of β*; ‘<i>Rest</i>’, analogue to ‘Assigned’, only with communities that were not assigned to original compotypes β*. Mean and standard deviations for ‘<i>Original</i>’ respectively are: 0.849±0.165, 0.856±0.145 and 0.813±0.216.</p

Network topology for assigned communities and rest, for the three community-detection algorithms (Louvain, top; Infomap, middle, OSLOM, bottom).

<p>(left) Node-betweenness-centrality [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.ref082" target="_blank">82</a>], normalized by dividing with (n-1)*(n-2), where n is number of nodes in a community. (right) Clustering-coefficient [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.ref083" target="_blank">83</a>]. Parameters were calculated using [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.ref084" target="_blank">84</a>].</p

Statistics related to communities and compotypes.

<p>Statistics related to communities and compotypes.</p

Examples of GARD simulations under different β’s.

<p>(A1-C1) Histories of different tapes; For each tape, assemblies from different generations are plotted along the X axis, and color represents the counts of each of the N_G molecule types in each assembly (recorded at assembly size N_max (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.g001" target="_blank">Fig 1</a>). Tapes are separated by a vertical black line. For each tape, the first 1,000 assemblies are shown. Red color represents counts ≥ 50, and for brevity counts < 5 are colored white. (A2-C2) Density plots; For each assembly shown in panels (A1-C1), its Euclidean distance and angle vs. the eigenvector of the full-β was calculated (normalized for the maximum value between two assemblies, for distance and 90 degrees for angle). Color is normalized probability (log₁₀ scale) of an assembly having a certain angle and distance. See section: Compotype-community assignment. (A3-C3) Same as (A2-C2), except for each assembly the distance and angle are calculated against the one eigenvector of β* which has the lowest angle to this assembly. Number of Infomap communities detected is: 9 (A3), 7 (B3) and 6 (C3). Further examples are available at <a href="http://ico2s.org/data/extras/gard/" target="_blank">http://ico2s.org/data/extras/gard/</a> and [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.ref073" target="_blank">73</a>].</p

Bar plot of the percentage of high compositional similarity (H, Eq 3) when predicting compotypes using the eigenvectors of β* (Eq 2) vs. full-β.

<p>Percentage is given out of the total number of compotypes observed under all β networks. Mean and standard deviation are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.t001" target="_blank">Table 1</a> and full histograms are given in Fig D in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.s001" target="_blank">S1 File</a>.</p

Schematics of GARD’s dynamics.

<p>Different molecules types (represented by different colored circles) aggregate to form assemblies. Aggregation is biased by a matrix of chemical rates (β, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192871#pone.0192871.e001" target="_blank">Eq 1</a>)). Once an assembly reaches a size-threshold (N_max) it splits, and the progeny then continues the growth-split cycles (generations). A composome is an assembly that has high average compositional similarity (see section: The GARD model) to its parent and to one of its children.</p

Overview of the algorithm developed in the present work.

<p>(<b>A</b>) A network (β) is employed in GARD simulations and the emerging compotype species are collected. (<b>B</b>) In parallel, the communities of β are analysed and collected. Finally, (A) and (B) are compared by using the ensemble of detected communities to predict compotypes.</p

Comparison of prediction methods.

<p>Results of a Friedman test to compare prediction methods across different datasets and feature selection methods (the best average ranks are shown in bold typeface; *here only the results in combination with feature selection are taken into account).</p