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

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

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

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

Study numbers, labels, number of samples and descriptions of the <i>Fusarium</i> microarray dataset.

<p>Study numbers, labels, number of samples and descriptions of the <i>Fusarium</i> microarray dataset.</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

Boxplot intra vs inter clusters correct-prediction.

<p>Boxplot intra vs inter clusters correct-prediction.</p