Additional file 1: Figure S1. of Arete – candidate gene prioritization using biological network topology with additional evidence types

Evaluation of performance for multi-disease and single-disease gene subsets. (PDF 183 kb

Flowchart of the steps for the pipeline.

<p>The figure shows the main steps that constitute the pipeline. Each step is properly described in this section.</p

TPs and FPs vs noise before calculating the correct-prediction.

<p>The figures show the evolution of TPs and FPs vs noise in terms of nodes (variables involved in the discovered subnetworks) and connections between nodes. These are the partial results, prior to the filtering of the informative nodes based on the intra cluster correct-prediction accuracy (which are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106524#pone-0106524-g006" target="_blank">Figure 6</a>).</p

Intra cluster correct-prediction distribution for 10, 50 and 90% perturbation.

<p>The figures show the histograms of the intra cluster correct-prediction (calculated within the same cluster using cross-validation) for the simulated dataset for different levels of noise.</p

Unique-Network for <i>Fusarium</i> cluster 2,5,6,7,13.

<p>In this figure grey background indicates highly predictive genes (average correct-prediction equal or higher than 0.6). Despite the lack of different conditions in the dataset, as explained in the text, still about a 1/3 of the genes selected are highly predictive.</p

Simulation studies generated independently from the three networks in consideration.

<p>Simulation studies generated independently from the three networks in consideration.</p

Intra cluster correct-prediction for simulated data.

<p>The figure shows the boxplots of the intra cluster correct-prediction (calculated within the same cluster using cross-validation) for the simulated dataset in the case of 0% of noise.</p

<i>Big matrix</i> constructed from the datasets generated from the three networks and six randomly generated datasets which represent the noise.

<p>The shaded regions indicate the non-noisy datasets generated from Alarm, Insurance and Child networks (respectively A, I and C in the figure).</p

Additional file 5: of Representing and querying disease networks using graph databases

Cypher query on the relationships between a) the O15534 protein (PER gene) and b) the P20393 protein (REV/ERBalpha gene) and the core clock genes, (Table 3). (DOCX 77 kb

Intra vs inter clusters prediction for <i>Fusarium</i>.

<p>Intra vs inter clusters prediction for <i>Fusarium</i>.</p